diff --git a/.github/workflows/cgatapps_python.yml b/.github/workflows/cgatapps_python.yml
index 115bc011b..44dde74b3 100644
--- a/.github/workflows/cgatapps_python.yml
+++ b/.github/workflows/cgatapps_python.yml
@@ -47,3 +47,4 @@ jobs:
           pip install nose
           nosetests -v tests/test_style.py
           nosetests -v tests/test_scripts.py
+          nosetests -v tests/test_import.py
\ No newline at end of file
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 000000000..e41dd8d21
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,73 @@
+name: Publish cgat-apps wheels to PyPI and TestPyPI
+
+on:
+  push:
+    branches:
+      - v[0-9]+.[0-9]+.x
+    tags:
+      - v*
+  release:
+    types:
+      - published
+
+jobs:
+
+  build_sdist:
+
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os: [ubuntu, macos]
+        python-version: [3.10]
+
+    steps:
+      - name: Checkout cgat-apps
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install prerequisite Python libraries
+        run:  |
+          python -m pip install --upgrade pip
+          pip install wheel
+
+      - name: Create source distribution
+        run:  python setup.py sdist bdist_wheel
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+      - uses: actions/upload-artifact@v2          
+        with:
+          path: dist/*.whl
+
+  upload_pypi:
+
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Get Artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish distribution to Test PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'published'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
diff --git a/COPYING b/COPYING
deleted file mode 100644
index e38022ec0..000000000
--- a/COPYING
+++ /dev/null
@@ -1,25 +0,0 @@
-Copyright 2010-2011 The Medical Research Council (MRC). All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-1. Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE MRC ``AS IS'' AND ANY EXPRESS OR
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE MRC OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
-GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/PKG-INFO b/PKG-INFO
deleted file mode 100644
index 583ea0cc1..000000000
--- a/PKG-INFO
+++ /dev/null
@@ -1,22 +0,0 @@
-Metadata-Version: 1.1
-Name: SphinxReport
-Version: 2.0
-Summary: SphinxReport : a report generator in python based on Sphinx and matplotlib
-Home-page: http://code.google.com/p/sphinx-report/
-Author: Andreas Heger
-Author-email: andreas.heger@gmail.com
-License: BSD
-Description: SphinxReport : a report generator in python based on Sphinx and matplotlib
-Keywords: report generator sphinx matplotlib sql
-Platform: any
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved
-Classifier: Programming Language :: Python
-Classifier: Topic :: Software Development
-Classifier: Topic :: Scientific/Engineering
-Classifier: Operating System :: Microsoft :: Windows
-Classifier: Operating System :: POSIX
-Classifier: Operating System :: Unix
-Classifier: Operating System :: MacOS
diff --git a/cgat/AGP.py b/cgat/AGP.py
index 305b1b16b..809b3366a 100644
--- a/cgat/AGP.py
+++ b/cgat/AGP.py
@@ -9,7 +9,22 @@
 
 """
 
+import functools
 
+
+def deprecated_class(cls):
+    orig_init = cls.__init__
+
+    @functools.wraps(orig_init)
+    def new_init(self, *args, **kwargs):
+        warnings.warn(f"{cls.__name__} is deprecated and will be removed in the next release.", DeprecationWarning)
+        orig_init(self, *args, **kwargs)
+
+    cls.__init__ = new_init
+    return cls
+
+
+@deprecated_class
 class ObjectPosition(object):
 
     def map(self, start, end):
@@ -19,6 +34,7 @@ def map(self, start, end):
             return end + self.start, start + self.start
 
 
+@deprecated_class
 class AGP(object):
     """Parser for AGP formatted files."""
 
diff --git a/cgat/CBioPortal.py b/cgat/CBioPortal.py
deleted file mode 100644
index f85f47115..000000000
--- a/cgat/CBioPortal.py
+++ /dev/null
@@ -1,1038 +0,0 @@
-'''CBioPortal.py - Interface with the Sloan-Kettering cBioPortal webservice
-========================================================================
-
-The Sloan Kettering cBioPortal webservice provides access to a
-database of results of genomics experiments on various cancers. The
-database is organised into studies, each study contains a number of
-case lists, where each list contains the ids of a set of patients, and
-genetic profiles, each of which represents an assay conducted on the
-patients in the case list as part of the study.
-
-The main class here is the CBioPortal class representing a connection
-to the cBioPortal Database. Query's are represented as methods of the
-class. Study ids or names or case lists can be provided to the
-constructor to the object, via the setDefaultStudy and
-setDefaultCaseList methods or to the indevidual query methods. Where
-ever possible the validity of parameters is checked *before* the query
-is executed.
-
-Whenever a query requires a genetic profile id or a list of such ids,
-but none are given, the list of all profiles for which the
-show_in_analysis flag is set will be used.
-
-All of the commands provided in the webservice are implemented here
-and as far as possible the name, syntax and paramter names of the
-query are identical to the raw commands to the webservice. These
-queries are:
-
-* getCancerStudies,
-* getCaseLists,
-* getProfileData,
-* getMutationData,
-* getClinicalData,
-* getProteinArrayInfo,
-* getProteinArrayData,
-* getLink,
-* getOncoprintHTML.
-
-In addition two new queries are implememented that are not part of the
-webservice:
-
-* getPercentAltered and
-* getTotalAltered
-
-These emulate the function of the website where the percent of cases
-that show any alteration for the gene and profiles given are returned
-(getPercentAltered, or the percent of cases that show an alteration in
-any of the genes (getTotalAltered) is returned.
-
-examples::
-
-   gene_list = [ "TP53",
-   "BCL2",
-   "MYC"  ]
-   portal = CBioPortal()
-   portal.setDefaultStudy(study = "prad_mskcc")
-   portal.setDefaultCaseList(case_set_id = "prad_all_complete")
-   portal.getPercentAltered(gene_list = gene_list)
-
-or more tersely::
-
-   portal.CBioProtal()
-   portal.getPercentAltered(study = "prad_mskcc", case_set_id = "prad_all_complete",
-                            gene_list = ["TP53","BCL2","MYC"],
-                            genetic_profile_id =["prad_mskcc_mrna"])
-
-Any warnings returned by the query are stored in CBioPortal.last_warnings.
-
-Query's that would give too long an URL are split into smaller querys
-and the results combined transparently.
-
-A commandline interface is provided for convenience, syntax::
-
-   python CBioPortal.py [options] command(s)
-
-Reference
----------
-
-'''
-from urllib.request import urlopen
-import re
-import optparse
-import sys
-from cgatcore import iotools as iotools
-from collections import OrderedDict as odict
-from cgatcore import experiment as E
-
-
-class CBioPortal():
-    """connect to the cBioPortal Database.
-
-    If no url is specified the default url is used. A list of of valid
-    study ids is retrieved from the database. This both confirms that
-    the datavase is reachable, and provides cached checking for the
-    ids provided. If a study or study name is provided then this is
-    set as the defualt study for this session and the details of the
-    availible profiles and cases is retrieved.  'Study' is the study
-    id. If both study and study_name are specified then the study id
-    is used.
-    """
-
-    url = "http://www.cbioportal.org/public-portal/webservice.do"
-
-    def __init__(self, url=None, study=None, study_name=None,
-                 case_list_id=None):
-
-        if url:
-            self.url = url
-
-        self.getCancerStudies()
-        self.study = None
-        self.case_list = None
-
-        if study:
-
-            if study in self._valid_study_ids:
-                self.study = study
-
-                self.profiles = self.getGeneticProfiles(study)
-                self.cases = self.getCaseLists(study)
-            else:
-                raise ValueError("%s is not a valid study id" % study)
-
-        elif study_name:
-            if study_name in [x['name'] for x in cancer_studies]:
-                study = [x['cancer_study_id']
-                         for x in cancer_studies if x['name'] == study_name][0]
-                self.study = study
-                self.profiles = self.getGeneticProfiles(study)
-                self.cases = self.getCaseLists(study)
-
-            else:
-                raise ValueError("%s is not a valid study name" % study_name)
-
-        if case_list_id:
-            self.setDefaultCaseList(case_list_id)
-
-    def _executeQuery(self, command, args=None):
-        """execute the provided command on the database.
-
-        args are specified as a dictionary.  error checking on the
-        results is performed here and the returned value is a list of
-        lists with each list representing a row of the returned table.
-        """
-        try:
-            argument_string = "&".join(["%s=%s" % (x, args[x]) for x in args])
-            command_string = "&".join([command, argument_string])
-        except TypeError:
-            command_string = command
-
-        query = "%s?cmd=%s" % (self.url, command_string)
-
-        if len(query) > 2048:
-            if "gene_list" in args:
-                genes = args['gene_list'].split(",")
-
-                if len(genes) < 2:
-                    raise ValueError("Request too long")
-
-                args['gene_list'] = ",".join(genes[(len(genes) / 2):])
-                query1 = self._executeQuery(command, args)
-                warnings = self.last_warnings
-
-                args['gene_list'] = ",".join(genes[:(len(genes) / 2)])
-                query2 = self._executeQuery(command, args)
-                self.last_warnings = warnings + self.last_warnings
-
-                return query1 + query2
-
-        data = urlopen(query)
-
-        line = data.readline()
-        self.last_query = query
-        self.last_status = line
-        self.last_warnings = []
-        self.last_header = [self.last_status]
-        return_table = []
-
-        while re.match("^#", line):
-
-            if re.match("^# Warning: (.+)", line):
-                self.last_warnings.append(
-                    re.match("^# Warning: (.+)", line).groups(1)[0])
-                self.last_header.append(line)
-                line = data.readline()
-                continue
-
-            elif re.match("^#", line):
-                self.last_header.append(line)
-                line = data.readline()
-                continue
-
-        if re.match("^Error: (.+)", line):
-            self.last_header.append(line)
-            raise CDGSError(re.match("^Error: (.+)", line).groups(1)[0], query)
-        line = line.strip()
-        headers = line.split("\t")
-
-        for line in data:
-            if re.match("^# Warning: (.+)", line):
-                self.last_warnings.append(
-                    re.match("^# Warning: (.+)", line).groups(1)[0])
-                self.last_header.append(line)
-                line = data.readline()
-                continue
-            line = line.strip()
-            return_table.append(odict(list(zip(headers, line.split("\t")))))
-
-        return return_table
-
-    def _getStudyId(self, study, study_name):
-
-        if study:
-            if study in self._valid_study_ids:
-                return study
-            else:
-                raise ValueError("%s is not a valid study id" % study)
-
-        elif study_name:
-            name_lookup = [x['study']
-                           for x in self.cancer_studies if x['name'] == study_name]
-            if len(name_lookup) == 1:
-                return name_lookup[0]
-            else:
-                raise ValueError(
-                    "Cannot find study id for study '%s'" % study_name)
-
-        elif self.study:
-            return self.study
-
-        else:
-            return None
-
-    def getCancerStudies(self):
-        """Fetches the list of cancer studies currently in the database.
-
-        Returns list of dictionaries with three entries
-        'cancer_study_id','name' and 'description'.  Also caches this
-        data to verify the validity of later calls
-        """
-        cancer_studies = self._executeQuery("getCancerStudies")
-        self.cancer_studies = cancer_studies
-        self._valid_study_ids = [x['cancer_study_id'] for x in cancer_studies]
-
-        return self.cancer_studies
-
-    def getGeneticProfiles(self, study=None, study_name=None):
-        """Fetches the valid genetic profiles for a particular study.
-
-        study is the study id.  If both study and study_name are
-        specified, study is used. If neither study nor study name is
-        specified then the default study is used if set, if not a
-        value error is raised.
-        Returns a list of dictionaries
-        """
-
-        study = self._getStudyId(study, study_name)
-
-        if not study:
-            raise ValueError("A study must be specified if no default is set")
-
-        genetic_studies = self._executeQuery(command="getGeneticProfiles",
-                                             args=dict(cancer_study_id=study))
-        return genetic_studies
-
-    def getCaseLists(self, study=None, study_name=None):
-        """Retrieves meta-data regarding all case lists stored about a
-        specific cancer study.
-
-        For example, a within a particular study, only some cases may
-        have sequence data, and another subset of cases may have been
-        sequenced and treated with a specific therapeutic
-        protocol. Multiple case lists may be associated with each
-        cancer study, and this method enables you to retrieve
-        meta-data regarding all of these case lists.
-
-        Data is returned as a list of dictionaries with the following
-        entries:
-
-         * case_list_id: a unique ID used to identify the case list ID
-           in subsequent interface calls. This is a human readable
-           ID. For example, "gbm_all" identifies all cases profiles in
-           the TCGA GBM study.
-
-         * case_list_name: short name for the case list.
-
-         * case_list_description: short description of the case list.
-
-         * cancer_study_id: cancer study ID tied to this genetic
-           profile. Will match the input cancer_study_id.
-
-         * case_ids: space delimited list of all case IDs that make up
-           this case list.
-        """
-
-        study = self._getStudyId(study, study_name)
-
-        if not study:
-            raise ValueError("A study must be specified if no default is set")
-
-        case_lists = self._executeQuery(
-            command="getCaseLists",
-            args=dict
-            ({'cancer_study_id': study}))
-        return case_lists
-
-    def getProfileData(self, gene_list, case_set_id=None,
-                       genetic_profile_id=None, study=None, study_name=None):
-        """Retrieves genomic profile data for one or more genes.
-
-        You can specify one gene and many profiles or one profile and
-        many genes.  If you specify no genetic profiles then all
-        genetic profiles for the specified or default study are used
-        if the case_set_id is from that study otherwise a ValueError
-        is raised.
-
-        Return value depends on the parameters. If you specify a
-        single genetic profile and multiple genes a list of ordered
-        dictionaries with the following entries::
-
-            gene_id: Entrez Gene ID
-            common: HUGO Gene Symbol
-            entries 3 - N: Data for each case
-
-        If you specify multi genetic profiles and a single gene, a
-        list of ordered dictoraries with the following entries is
-        returned::
-
-            genetic_profile_id: The Genetic Profile ID.
-            alteration_type: The Genetic Alteration Type, e.g. MUTATION, MUTATION_EXTENDED, COPY_NUMBER_ALTERATION, or MRNA_EXPRESSION.
-            gene_id: Entrez Gene ID.
-            common: HUGO Gene Symbol.
-            Columns 5 - N: Data for each case.
-
-        """
-
-        # Do some pre-query checking.
-
-        if len(gene_list) > 1 and len(genetic_profile_id) > 1:
-            raise ValueError(
-                "%i genes and %i profiles specified\n.Please "
-                "specify either one gene many profiles or one "
-                "profile many genes" % (
-                    len(gene_list), len(genetic_profile_id)))
-
-        study_id = self._getStudyId(study, study_name)
-        case_set_id = self._getCaseListId(case_set_id, study_id)
-
-        genetic_profile_id = self._getAndCheckGeneticProfiles(
-            genetic_profile_id=genetic_profile_id, study=study)
-
-        gene_list = ",".join(gene_list)
-        genetic_profile_id = ",".join(genetic_profile_id)
-
-        profile_data = self._executeQuery(
-            command="getProfileData",
-            args={'case_set_id': case_set_id,
-                  'genetic_profile_id': genetic_profile_id,
-                  'gene_list': gene_list})
-
-        return profile_data
-
-    def getMutationData(self, gene_list, genetic_profile_id, case_set_id=None,
-                        study=None, study_name=None):
-        '''For data of type EXTENDED_MUTATION, you can request the full set of
-        annotated extended mutation data.
-
-        This enables you to, for example, determine which sequencing
-        center sequenced the mutation, the amino acid change that
-        results from the mutation, or gather links to predicted
-        functional consequences of the mutation.
-
-        Query Format
-
-
-            case_set_id= [case set ID] (required)
-            genetic_profile_id= [a single genetic profile IDs] (required).
-            gene_list= [one or more genes, specified as HUGO Gene Symbols or
-                 Entrez Gene IDs](required)
-
-        Response Format
-
-        A list of dictionaries with the following entires
-
-            entrez_gene_id: Entrez Gene ID.
-            gene_symbol: HUGO Gene Symbol.
-            case_id: Case ID.
-            sequencing_center: Sequencer Center responsible for identifying
-                this mutation.
-                               For example: broad.mit.edu.
-            mutation_status: somatic or germline mutation status. all mutations
-                         returned will be of type somatic.
-            mutation_type: mutation type, such as nonsense, missense, or frameshift_ins.
-            validation_status: validation status. Usually valid, invalid, or unknown.
-            amino_acid_change: amino acid change resulting from the mutation.
-
-            functional_impact_score: predicted functional impact score,
-                 as predicted by: Mutation Assessor.
-            xvar_link: Link to the Mutation Assessor web site.
-            xvar_link_pdb: Link to the Protein Data Bank (PDB) View within
-                       Mutation Assessor web site.
-            xvar_link_msa: Link the Multiple Sequence Alignment (MSA) view
-                 within the Mutation Assessor web site.
-            chr: chromosome where mutation occurs.
-            start_position: start position of mutation.
-            end_position: end position of mutation.
-
-        If a default study is set then a check will be performed to
-        set if the supplied case id is from the specified study. The
-        study can be over written using the study and study_name
-        parameters
-
-        '''
-
-        study_id = self._getStudyId(study, study_name)
-
-        case_set_id = self._getCaseListId(case_set_id, study_id)
-
-        if study_id:
-            if not study_id == self.study:
-                profiles = getGeneticProfiles(study_id)
-            else:
-                profiles = self.profiles
-
-            if genetic_profile_id not in proiles:
-                raise ValueError(
-                    "%s not a valid genetic profile for study %s" %
-                    (genetic_profile_id, gene_id))
-        genetic_profile_id = ",".join(genetic_profile_id)
-        gene_list = ",".join(gene_list)
-        mutation_data = self._executeQuery(
-            command="getMutationData",
-            args=dict({"case_set_id": case_set_id,
-                       "genetic_profile_id": genetic_profile_id,
-                       "gene_list": gene_list}))
-        return mutation_data
-
-    def getClinicalData(self, case_set_id=None, study=None, study_name=None):
-        '''Retrieves overall survival, disease free survival and age at
-        diagnosis for specified cases.
-
-        Due to patient privacy restrictions, no other clinical data is
-        available.
-
-        Query Format
-        ------------
-
-            case_set_id= [case set ID] (required)
-
-        Response Format
-        ---------------
-
-        A list of dictionaries with the following entries:
-
-            case_id: Unique Case Identifier.
-            overall_survival_months: Overall survival, in months.
-            overall_survival_status: Overall survival status, usually
-                 indicated as "LIVING" or "DECEASED".
-            disease_free_survival_months: Disease free survival, in months.
-            disease_free_survival_status: Disease free survival status,
-                 usually indicated as "DiseaseFree" or "Recurred/Progressed".
-            age_at_diagnosis: Age at diagnosis.
-
-        If a study is specified or a defualt study is set, then the
-        case_set_id will be tested to check if it exists for that
-        study.
-
-        '''
-
-        study_id = self._getStudyId(study, study_name)
-
-        case_set_id = self._getCaseListId(case_set_id, study_id)
-
-        clincal_data = self._executeQuery(
-            command="getClinicalData",
-            args=dict({'case_set_id': case_set_id}))
-        return clincal_data
-
-    def getProteinArrayInfo(self, protein_array_type=None, gene_list=None,
-                            study=None, study_name=None):
-        '''Retrieves information on antibodies used by reverse-phase protein
-        arrays (RPPA) to measure protein/phosphoprotein levels.
-
-        Query Format
-        ------------
-
-            cancer_study_id= [cancer study ID] (required)
-            protein_array_type= [protein_level or phosphorylation]
-            gene_list= [one or more genes, specified as HUGO Gene
-            Symbols or Entrez Gene IDs].
-
-        Response Format
-        ---------------
-
-        A list of dictionaries with the following entires:
-
-            ARRAY_ID: The protein array ID.
-            ARRAY_TYPE: The protein array antibody type, i.e. protein_level
-                or phosphorylation.
-            GENE: The targeted gene name (HUGO gene symbol).
-            RESIDUE: The targeted resdue(s).
-
-        If no study is specified the default study is used. If that is
-        not specified an error is raised.
-
-        '''
-
-        study = self._getStudyId(study, study_name)
-        args = dict({'cancer_study_id': study})
-
-        if gene_list:
-            args['gene_list'] = ",".join(gene_list)
-
-        if protein_array_type:
-            args['protein_array_type'] = protein_array_type
-
-        protein_array_info = self._executeQuery(
-            command="getProteinArrayInfo", args=args)
-
-        return protein_array_info
-
-    def getProteinArrayData(self, protein_array_id=None, case_set_id=None,
-                            array_info=0, study=None, study_name=None):
-        '''Retrieves protein and/or phosphoprotein levels measured by
-        reverse-phase protein arrays (RPPA).
-
-        Query Format
-        ------------
-
-        case_set_id= [case set ID]
-        protein_array_id= [one or more protein array IDs] as list.
-        array_info= [1 or 0]. If 1, antibody information will also be exported.
-
-        Response Format 1
-        -----------------
-
-        If the parameter of array_info is not specified or it is not
-        1, returns a list of dictionaries with the following columns.
-
-        ARRAY_ID: The protein array ID.
-        Columns 2 - N: Data for each case.
-
-        Response Format 2
-        -----------------
-
-        If the parameter of array_info is 1, you will receive a list
-        of ordered dictionaries with the following entires:
-
-        ARRAY_ID: The protein array ID.
-        ARRAY_TYPE: The protein array antibody type, i.e. protein_level or
-             phosphorylation.
-        GENE: The targeted gene name (HUGO gene symbol).
-        RESIDUE: The targeted resdue(s).
-        Columns 5 - N: Data for each case.
-
-        If the defualt study is set then the case_set_id will be
-        check. The default study can be overidden using the study or
-        study_name parameters.
-
-        '''
-
-        study_id = self._getStudyId(study, study_name)
-
-        case_set_id = self._getCaseListId(case_set_id, study_id)
-        args = dict({"case_set_id": case_set_id,
-                     "array_info": array_info})
-
-        if protein_array_id:
-            args['protein_array_id'] = ",".join(protein_array_id)
-
-        protein_array_data = self._executeQuery(
-            command="getProteinArrayData", args=args)
-
-        return protein_array_data
-
-    def getLink(self, gene_list, study=None, study_name=None,  report="full"):
-        '''return a perminant link to the cBioPortal report for the gene_list
-            cancer_study_id=[cancer study ID] gene_list=[a comma
-            separated list of HUGO gene symbols] (required)
-            report=[report to display; can be one of: full (default),
-            oncoprint_html]
-        '''
-
-        study = self._getStudyId(study, study_name)
-        if not study:
-            raise ValueError("Study must be specified")
-        if report not in ["full", "oncoprint_html"]:
-            raise ValueError("%s is not a valid report" % report)
-
-        url = "/".join(self.url.split("/")[:-1])
-
-        gene_list = ",".join(gene_list)
-        return "%s/link.do?cancer_study_id=%s&gene_list=%s&report=%s" %\
-            (url, study, gene_list, report)
-
-    def getOncoprintHTML(self, gene_list, study=None, study_name=None):
-        '''returns the HTML for the oncoprint report for the specified gene
-        list and study'''
-
-        url = "/".join(self.url.split("/")[0:-1])
-        gene_list = ",".join(gene_list)
-        command = "%s/link.do?cancer_study_id=%s&gene_list=%s&report=oncoprint_html" % (
-            url, study, gene_list)
-        return urlopen(command).read()
-
-    def setDefaultStudy(self, study=None, study_name=None):
-        '''sets a new study as the default study. Will check that the study
-        id is valid'''
-        study = self._getStudyId(study, study_name)
-        self.study = study
-        self.profiles = self.getGeneticProfiles()
-        self.cases = self.getCaseLists()
-
-        all_case_list = [x['case_list_id']
-                         for x in self.cases
-                         if x['case_list_name'] == "All Tumours"]
-
-        if len(all_case_list) == 1:
-            self.setDefaultCaseList(all_case_list)
-
-    def setDefaultCaseList(self, case_set_id, study=None, study_name=None):
-        '''set the default case list. If study is not specified the default
-        study will be used.
-
-        The study will be used to check that the case_set exists.
-        '''
-
-        study = self._getStudyId(study, study_name)
-        case_list = self._getCaseListId(case_set_id, study=study)
-
-        if not study == self.study:
-            self.setDefaultStudy(study)
-
-        self.case_list = case_list
-
-    def _getCaseListId(self, case_set_id=None, study=None, strict=True):
-        ''' checking is only done if study is specified or a default is set '''
-
-        study_id = self._getStudyId(study, None)
-
-        if case_set_id:
-            if study_id:
-                if not study_id == self.study:
-                    case_lists = [x['case_list_id']
-                                  for x in self.getCaseLists(study_id)]
-                else:
-                    case_lists = [x['case_list_id'] for x in self.cases]
-
-                if case_set_id not in case_lists:
-                    raise ValueError(
-                        "%s is not a valid case list for study %s" % (case_set_id, study_id))
-            return case_set_id
-
-        else:
-            if self.case_list:
-                return self.case_list
-            else:
-                raise ValueError("No case_set_id provided and no default set")
-
-    def _getAndCheckGeneticProfiles(self, genetic_profile_id=None, study=None):
-
-        study_id = self._getStudyId(study, None)
-        if not genetic_profile_id:
-            if not study_id:
-                raise ValueError(
-                    "Either genetic_profile_id or study must be specified")
-
-            if study_id == self.study:
-                genetic_profile_id = [x['genetic_profile_id']
-                                      for x in self.profiles
-                                      if x['show_profile_in_analysis_tab'] == "true"]
-            else:
-                genetic_profile_id = [x['genetic_profile_id']
-                                      for x in self.getGeneticProfiles(study_id)
-                                      if x['show_profile_in_analysis_tab'] == "true"]
-
-            return genetic_profile_id
-
-        else:
-
-            if not study_id:
-                return genetic_profile_id
-
-            if study_id == self.study:
-                genetic_profile_id = [x['genetic_profile_id'] for x in self.profiles
-                                      if x['genetic_profile_id'] in genetic_profile_id]
-            else:
-                genetic_profile_id = [x['genetic_profile_id'] for x in self.getGeneticProfiles(study_id)
-                                      if x['genetic_profile_id'] in genetic_profile_id]
-
-            if len(genetic_profile_id) == 0:
-                raise ValueError("no valid genetic_profile_ids found")
-
-            return genetic_profile_id
-
-    def getPercentAltered(self, gene_list, study=None, study_name=None,
-                          case_set_id=None, genetic_profile_id=None,
-                          threshold=2):
-        '''Get the percent of cases that have one or more of the specified
-        alterations for each gene
-
-        Query Format
-        ------------
-
-        study = [cancer_study_id] The study to use.
-
-        study_name = [cancer_study_name] The name of the study to
-                     use. If neither this nor study are specified,
-                     then the default is used.
-
-        case_set_id = [case_set_id] The case list to use. If not
-                      specified, the default case list is used.
-
-        gene_list = [one or more genes, specified as HUGO Gene Symobls
-        or ENtrez Gene IDs] (require)
-
-        genetic_profile_id = [one or more genetic profile IDs] If none
-        specified all genetic profiles for the specified study are
-        used..
-
-        threhold = [z_score_threshold] the numeric threshold at which
-        a mrna expression z-score is said to be significant.
-
-        Response Format
-        ---------------
-
-        A list of dictionaries with the following entries
-        gene_id: The Entrez Gene ID
-        common: The Hugo Gene Symbol
-        altered_in: The percent of cases in which the gene is altered
-
-        One implementation note is that a guess must be made as to
-        wether a returned profile value represents a alteration or
-        not. Currently guesses are only made for copy number
-        variation, mrna expression and mutionation
-
-        '''
-
-        study = self._getStudyId(study, study_name)
-        case_set_id = self._getCaseListId(case_set_id, study)
-        genetic_profile_id = self._getAndCheckGeneticProfiles(
-            genetic_profile_id, study)
-
-        if study and study == self.study:
-            profiles = self.profiles
-            case_list = [x['case_ids']
-                         for x in self.cases
-                         if x['case_list_id'] == case_set_id][0]
-
-        else:
-            profiles = self.getGeneticProfiles(study)
-            case_list = [x['case_ids'] for x in self.getCaseLists(
-                study) if x['case_list_id'] == case_set_id][0]
-
-        return_table = []
-        case_list = case_list.split(" ")
-
-        data = []
-        warnings = []
-        for profile in genetic_profile_id:
-
-            data.append(self.getProfileData(
-                gene_list=gene_list, case_set_id=case_set_id,
-                genetic_profile_id=[profile]))
-            warnings.extend(self.last_warnings)
-
-        # data[profile][gene][case]
-        for gene in range(len(data[0])):
-            cases_altered = 0.0
-
-            geneProfile = [x[gene] for x in data]
-
-            for case in (set(geneProfile[0]) - set(["gene_id", "common"])):
-                if len([geneProfile[x][case] for x in range(len(geneProfile))
-                        if self._guessAlteration(
-                            geneProfile[x][case],
-                            genetic_profile_id[x], profiles)]) > 0:
-
-                    cases_altered += 1
-
-            return_table.append(
-                dict({'gene_id': geneProfile[0]['GENE_ID'],
-                      'common': geneProfile[0]['COMMON'],
-                      'altered_in': cases_altered * 100 / len(case_list)}))
-
-        self.last_warnings = warnings
-        return return_table
-
-    def getTotalAltered(self, gene_list, study=None, study_name=None, case_set_id=None, genetic_profile_id=None, threshold=2):
-        ''' Calculate the percent of cases in which any one of the specified genes are altered '''
-
-        study = self._getStudyId(study, study_name)
-        case_set_id = self._getCaseListId(case_set_id, study)
-        genetic_profile_id = self._getAndCheckGeneticProfiles(
-            genetic_profile_id, study)
-
-        if study == self.study:
-            profiles = self.profiles
-            case_list = [x['case_ids']
-                         for x in self.cases if x['case_list_id'] == case_set_id][0]
-        else:
-            profiles = self.getGeneticProfiles(study)
-            case_list = [x['case_ids'] for x in self.getCaseLists(
-                study) if x['case_list_id'] == case_set_id][0]
-        case_list = case_list.split(" ")
-
-        data = []
-
-        # data[gene][profile][case]
-        cases_altered = 0.0
-        for gene in gene_list:
-            data.append(self.getProfileData(
-                gene_list=[gene], case_set_id=case_set_id,
-                genetic_profile_id=genetic_profile_id))
-            # catch special case where only a single
-            # genetic_profile_id is passed in, so the query is single
-            # gene and single profile and returns genes as columns
-            # format.
-            if len(genetic_profile_id) == 1 and len(data[0]) == 1:
-                data[0][0]['GENETIC_PROFILE_ID'] = genetic_profile_id[0]
-
-        for case_id in set(data[0][0]) - set(
-                ["GENETIC_PROFILE_ID", "ALTERATION_TYPE",
-                 "GENE_ID", "COMMON"]):
-
-            case_altered = False
-            for gene in data:
-
-                altered = len([x for x in gene
-                               if self._guessAlteration(x[case_id],
-                                                        x['GENETIC_PROFILE_ID'],
-                                                        profiles, threshold)])
-                if (altered > 0):
-                    case_altered = True
-
-            if case_altered is True:
-                cases_altered += 1.0
-
-        return cases_altered * 100 / len(case_list)
-
-    def _guessAlteration(self, value, genetic_profile_id, genetic_profiles,
-                         threshold=2):
-
-        alteration_type = [x['genetic_alteration_type']
-                           for x in genetic_profiles
-                           if x['genetic_profile_id'] == genetic_profile_id][0]
-
-        # print alteration_type
-        if alteration_type == "COPY_NUMBER_ALTERATION":
-            if value == "0" or value == "-1" or value == "1":
-                return False
-            elif value == "NaN":
-                return False
-            else:
-                return True
-
-        elif alteration_type == "MRNA_EXPRESSION":
-            if re.search("[^0-9\.\-]", value):
-                # is character string
-                return False
-            elif re.search("[0-9]+\.[0-9]+", value):
-                # is float
-                value = float(value)
-                if abs(value) > threshold:
-                    return True
-                else:
-                    return False
-            else:  # must be int?
-                # print value
-                if value == "0":
-                    return False
-                else:
-                    return True
-
-        elif alteration_type == "METHYLATION":
-            return False
-
-        elif (alteration_type == "MUTATION" or
-              alteration_type == "MUTATION_EXTENDED"):
-            if value == "NaN":
-                return False
-            else:
-                return True
-        else:
-            return False
-
-
-class CDGSError(Exception):
-
-    '''exception that handles errors returned by querys in the database'''
-
-    def __init__(self, error, request):
-        self.error = error
-        self.request = request
-
-    def __str__(self):
-        return "Request %s return error:\n%s" % (self.request, self.error)
-
-
-def tableToString(intable):
-
-    headers = "\t".join([x for x in intable[0]])
-
-    line_list = []
-    for line in intable:
-
-        line_list.append("\t".join([str(line[x]) for x in line]))
-
-    outTable = "\n".join(line_list)
-    outTable = headers + "\n" + outTable
-
-    return outTable
-
-
-def main(argv=None):
-
-    parser = E.OptionParser(
-        version="%prog version: $Id$",
-        usage=globals()["__doc__"])
-
-    parser.add_option("-o", "--output_file", type="string", default=None,
-                      help="[Optional] Filename to output results to. [default=STDOUT]")
-    parser.add_option("-u", "--url", type="string", default="http://www.cbioportal.org/public-portal/webservice.do",
-                      help="[Optional] Url to the cBioPortal webservice [default=%default]")
-
-    cqueryopts = optparse.OptionGroup(
-        parser, "Common parameters", "Common arguments to the query")
-    cqueryopts.add_option("-s", "--study_id", dest="study_id", type="string", default=None,
-                          help="[Required/OPtional]  cBioPortal ID for study [default=%default].\n This or study_name required for: getGeneticProfiles, getCaseLists, getProteinArrayInfo, getLink,getOncoprintHTML, getPercentAltered, getTotalAltered")
-    cqueryopts.add_option("-n", "--study_name", dest="study_name", type="string", default=None,
-                          help="[Required/Optional] cBioPortal Name for study [defualt=%default].\n See above for which commands require this.")
-    cqueryopts.add_option("-c", "--case_set_id", dest="case_set_id", type="string", default=None,
-                          help="[Required for some] cBioPortal case_set_id specifying the case list to use.\nRequired for getProfileData, getMutationData, getClincalData, getProteinArrayData, getPercentAltered, getTotalAltered. Default is case_set_id for case list 'All Tumours' ")
-    cqueryopts.add_option("-g", "--gene_list", dest="gene_list", type="string", default=None,
-                          help="[Required for some] Comma seperated list of HUGO gene symbols or Entrez gene IDs.\nRequired for getProfileData, getMutationData, getLink, getOncoprintHTML")
-    cqueryopts.add_option("-f", "--gene_list_file", dest="gene_list_file", type="string", default=None,
-                          help="[Optional] Filename to read in gene_list from")
-    cqueryopts.add_option("-p", "--profile_id", dest="profile_id", type="string",
-                          help="[Optional] Comma seperated list of cBioPortal genetic_profile_ids. If none are specified then the list of profiles for the study where display in analysis is True is used.")
-
-    squeryopts = optparse.OptionGroup(
-        parser, "Query specific parameters", "Arguments specific to a particular query")
-    squeryopts.add_option("--protein_array_type", dest="protein_array_type", type="string", default="protein_level",
-                          help="[Optional] Either protein_level or phosphorylation [default=%default]")
-    squeryopts.add_option("--protein_array_id", dest="protein_array_id", type="string",
-                          help="[Required for some] comma seperated list of one or more protein array IDs")
-    squeryopts.add_option("--array_info", dest="protein_array_info", type="int",  default=0,
-                          help="[Optional] If 1, antibody infomation will also be exported in a getProteinArrayData query [default=%default]")
-    squeryopts.add_option("--output-report", dest="report", type="string", default="full",
-                          help="[Optional] Report type to display for getLink. Either full or oncoprint_html [default=%default] ")
-    squeryopts.add_option("--threshold", dest="threshold", type="int", default=2,
-                          help="[Optional] Threshold for deciding if an alteration is significant for continuous metrics [default=%default]")
-
-    parser.add_option_group(cqueryopts)
-    parser.add_option_group(squeryopts)
-
-    (options, args) = E.Start(
-        parser, add_pipe_options=False, add_output_options=False, argv=argv)
-
-    portal = CBioPortal(url=options.url, study=options.study_id,
-                        study_name=options.study_name, case_list_id=options.case_set_id)
-
-    results = []
-
-    if options.gene_list_file:
-        infile = iotools.open_file(options.gene_list_file)
-        gene_list = [x.strip() for x in infile]
-    elif options.gene_list:
-        gene_list = options.gene_list.split(",")
-
-    if options.profile_id:
-        profile_id = options.profile_id.split(",")
-    else:
-        profile_id = None
-
-    if "getCancerStudies" in args:
-        results.append(portal.getCancerStudies())
-
-    if "getGeneticProfiles" in args:
-        results.append(portal.getGeneticProfiles())
-
-    if "getCaseLists" in args:
-        results.append(portal.getCaseLists())
-
-    if "getProfileData" in args:
-        results.append(
-            portal.getProfileData(gene_list=gene_list,
-                                  genetic_profile_id=profile_id))
-
-    if "getMutationData" in args:
-        results.append(
-            portal.getMutationData(gene_list=gene_list,
-                                   genetic_profile_id=profile_id))
-
-    if "getClinicalData" in args:
-        results.append(portal.getClinicalData())
-
-    if "getProteinArrayInfo" in args:
-        results.append(portal.getProteinArrayInfo(
-            gene_list=gene_list,
-            protein_array_type=options.protein_array_type))
-
-    if "getProteinArrayData" in args:
-        results.append(portal.getProteinArrayData(
-            protein_array_id=options.protein_array_id,
-            array_info=options.array_info))
-
-    if "getPercentAltered" in args:
-        results.append(portal.getPercentAltered(
-            gene_list=gene_list, genetic_profile_id=profile_id,
-            threshold=options.threshold))
-
-    if "getLink" in args:
-        results.append(
-            portal.getLink(gene_list=gene_list, report=options.report))
-
-    if "getOncoprintHTML" in args:
-        results.append(portal.getOncoprintHTML(gene_list=gene_list))
-
-    if len(results) == 0:
-        sys.stderr.write("No recognised query commands provided")
-        sys.exit()
-
-    if options.output_file:
-        outf = iotools.open_file(options.output_file, "w")
-    else:
-        outf = sys.stdout
-
-    for result in results:
-        try:
-            outf.write(tableToString(result))
-        except:
-            outf.write(result)
-
-    E.Stop()
-
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))
diff --git a/cgat/IGV.py b/cgat/IGV.py
deleted file mode 100644
index ebf5053e8..000000000
--- a/cgat/IGV.py
+++ /dev/null
@@ -1,169 +0,0 @@
-'''
-IGV.py - Simple wrapper to the IGV socket interface
-====================================================
-
-:Tags: Python
-
-This code was written by Brent Pedersen.
-
-Downloaded from https://github.com/brentp/bio-playground/blob/master/igv/igv.py
-on Nov.30 2011.
-
-'''
-
-import socket
-import os.path as op
-import os
-import subprocess
-import time
-
-
-def startIGV(command="igv.sh", port=None):
-    """start IGV on a specific port."""
-    args = [command]
-    if port is not None:
-        args.extend(['-p', str(port)])
-    process = subprocess.Popen(args,
-                               stdout=subprocess.PIPE)
-    time.sleep(10)
-    return process
-
-
-class IGV(object):
-    r"""
-    Simple wrapper to the IGV (http://www.broadinstitute.org/software/igv/home)
-    socket interface (http://www.broadinstitute.org/software/igv/PortCommands)
-
-    requires:
-
-        1) you have IGV running on your machine (launch with webstart here:
-                http://www.broadinstitute.org/software/igv/download)
-
-        2) you have enabled port communication in
-                View -> Preferences... -> Advanced
-
-    Successful commands return 'OK'
-
-    example usage:
-
-        >>> igv = IGV()
-        >>> igv.genome('hg19')
-        'OK'
-
-        >>> igv.load('http://www.broadinstitute.org/igvdata/1KG/pilot2Bams/NA12878.SLX.bam')
-        'OK'
-        >>> igv.go('chr1:45,600-45,800')
-        'OK'
-
-    #save as svg, png, or jpg
-        >>> igv.save('/tmp/r/region.svg')
-        'OK'
-        >>> igv.save('/tmp/r/region.png')
-        'OK'
-
-    # go to a gene name.
-        >>> igv.go('muc5b')
-        'OK'
-        >>> igv.sort()
-        'OK'
-        >>> igv.save('muc5b.png')
-        'OK'
-
-    # get a list of commands that will work as an IGV batch script.
-        >>> print "\n".join(igv.commands)
-        snapshotDirectory /tmp/igv
-        genome hg19
-        goto chr1:45,600-45,800
-        snapshotDirectory /tmp/r
-        snapshot region.svg
-        snapshot region.png
-        goto muc5b
-        sort base
-        snapshot muc5b.png
-
-    Note, there will be some delay as the browser has to load the annotations
-    at each step.
-
-    """
-    _socket = None
-    _path = None
-
-    def __init__(self, host='127.0.0.1', port=60151, snapshot_dir='/tmp/igv'):
-        self.host = host
-        self.port = port
-        self.commands = []
-        self.connect()
-        self.set_path(snapshot_dir)
-
-    @classmethod
-    def start(cls, jnlp="igv.jnlp",
-              url="http://www.broadinstitute.org/igv/projects/current/"):
-        import subprocess
-        p = subprocess.Popen("/usr/bin/javaws -Xnosplash %s%s" % (url, jnlp),
-                             shell=True, stdout=subprocess.PIPE)
-        p.wait()
-        return p.returncode
-
-    def connect(self):
-        if self._socket:
-            self._socket.close()
-        self._socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-        self._socket.connect((self.host, self.port))
-
-    def go(self, position):
-        return self.send('goto ' + position)
-    goto = go
-
-    def genome(self, name):
-        return self.send('genome ' + name)
-
-    def load(self, url):
-        return self.send('load ' + url)
-
-    def sort(self, option='base'):
-        """
-        options is one of: base, position, strand, quality, sample, and
-        readGroup.
-        """
-        assert option in ("base", "position", "strand", "quality", "sample",
-                          "readGroup")
-        return self.send('sort ' + option)
-
-    def set_path(self, snapshot_dir):
-        if snapshot_dir == self._path:
-            return
-        if not op.exists(snapshot_dir):
-            os.makedirs(snapshot_dir)
-
-        self.send('snapshotDirectory %s' % snapshot_dir)
-        self._path = snapshot_dir
-
-    def expand(self, track):
-        self.send('expand %s' % track)
-
-    def collapse(self, track):
-        self.send('collapse %s' % track)
-
-    def clear(self):
-        self.send('clear')
-
-    def send(self, cmd):
-        self.commands.append(cmd)
-        self._socket.send(cmd + '\n')
-        return self._socket.recv(10).rstrip('\n')
-
-    def save(self, path=None):
-        if path is not None:
-            # igv assumes the path is just a single filename, but
-            # we can set the snapshot dir. then just use the filename.
-            dirname = op.dirname(path)
-            if dirname:
-                self.set_path(dirname)
-            return self.send('snapshot ' + op.basename(path))
-        else:
-            return self.send('snapshot')
-    snapshot = save
-
-if __name__ == "__main__":
-    import doctest
-    doctest.testmod()
diff --git a/cgat/SVGdraw.py b/cgat/SVGdraw.py
deleted file mode 100644
index aee891935..000000000
--- a/cgat/SVGdraw.py
+++ /dev/null
@@ -1,1155 +0,0 @@
-'''
-SVGdraw.py - generate SVG drawings
-======================================================
-
-:Tags: Python
-
-This module has been copied from 3rd party resources.
-
-SVGdraw uses an object model drawing and a method toXML to create SVG graphics
-by using easy to use classes and methods usualy you start by creating a drawing eg
-
-    d=drawing()
-    #then you create a SVG root element
-    s=svg()
-    #then you add some elements eg a circle and add it to the svg root element
-    c=circle()
-    #you can supply attributes by using named arguments.
-    c=circle(fill='red',stroke='blue')
-    #or by updating the attributes attribute:
-    c.attributes['stroke-width']=1
-    s.addElement(c)
-    #then you add the svg root element to the drawing
-    d.setSVG(s)
-    #and finaly you xmlify the drawing
-    d.toXml()
-    
-
-this results in the svg source of the drawing, which consists of a circle
-on a white background. Its as easy as that;)
-This module was created using the SVG specification of www.w3c.org and the
-O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
-is available from www.adobe.com
-'''
-
-from io import StringIO
-import sys
-
-__version__ = "1.0"
-
-use_dom_implementation = 0
-
-if use_dom_implementation != 0:
-    try:
-        from xml.dom import implementation
-        from xml.dom.ext import PrettyPrint
-    except:
-        raise ImportError("PyXML is required for using the dom implementation")
-
-
-sys.setrecursionlimit = 50
-
-
-def _escape(data, entities={}):
-    """Escape &, <, and > in a string of data.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    data = data.replace("&", "&amp;")
-    data = data.replace("<", "&lt;")
-    data = data.replace(">", "&gt;")
-    for chars, entity in list(entities.items()):
-        data = data.replace(chars, entity)
-    return data
-
-
-def _quoteattr(data, entities={}):
-    """Escape and quote an attribute value.
-
-    Escape &, <, and > in a string of data, then quote it for use as
-    an attribute value.  The \" character will be escaped as well, if
-    necessary.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    data = _escape(data, entities)
-    if '"' in data:
-        if "'" in data:
-            data = '"%s"' % data.replace('"', "&quot;")
-        else:
-            data = "'%s'" % data
-    else:
-        data = '"%s"' % data
-    return data
-
-
-def _xypointlist(a):
-    """formats a list of xy pairs"""
-    s = ''
-    for e in a:  # this could be done more elegant
-        s += str(e)[1:-1] + '  '
-    return s
-
-
-def _viewboxlist(a):
-    """formats a tuple"""
-    s = ''
-    for e in a:
-        s += str(e) + ' '
-    return s
-
-
-def _pointlist(a):
-    """formats a list of numbers"""
-    return str(a)[1:-1]
-
-
-class pathdata:
-
-    """class used to create a pathdata object which can be used for a path.
-    although most methods are pretty straightforward it might be useful to look at the SVG specification."""
-    # I didn't test the methods below.
-
-    def __init__(self, x=None, y=None):
-        self.path = []
-        if x is not None and y is not None:
-            self.path.append('M ' + str(x) + ' ' + str(y))
-
-    def closepath(self):
-        """ends the path"""
-        self.path.append('z')
-
-    def move(self, x, y):
-        """move to absolute"""
-        self.path.append('M ' + str(x) + ' ' + str(y))
-
-    def relmove(self, x, y):
-        """move to relative"""
-        self.path.append('m ' + str(x) + ' ' + str(y))
-
-    def line(self, x, y):
-        """line to absolute"""
-        self.path.append('L ' + str(x) + ' ' + str(y))
-
-    def relline(self, x, y):
-        """line to relative"""
-        self.path.append('l ' + str(x) + ' ' + str(y))
-
-    def hline(self, x):
-        """horizontal line to absolute"""
-        self.path.append('H' + str(x))
-
-    def relhline(self, x):
-        """horizontal line to relative"""
-        self.path.append('h' + str(x))
-
-    def vline(self, y):
-        """verical line to absolute"""
-        self.path.append('V' + str(y))
-
-    def relvline(self, y):
-        """vertical line to relative"""
-        self.path.append('v' + str(y))
-
-    def bezier(self, x1, y1, x2, y2, x, y):
-        """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C' + str(x1) + ',' + str(y1) + ' ' +
-                         str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
-
-    def relbezier(self, x1, y1, x2, y2, x, y):
-        """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c' + str(x1) + ',' + str(y1) + ' ' +
-                         str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
-
-    def smbezier(self, x2, y2, x, y):
-        """smooth bezier with xy2 to xy absolut"""
-        self.path.append(
-            'S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
-
-    def relsmbezier(self, x2, y2, x, y):
-        """smooth bezier with xy2 to xy relative"""
-        self.path.append(
-            's' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
-
-    def qbezier(self, x1, y1, x, y):
-        """quadratic bezier with xy1 to xy absolut"""
-        self.path.append(
-            'Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
-
-    def relqbezier(self, x1, y1, x, y):
-        """quadratic bezier with xy1 to xy relative"""
-        self.path.append(
-            'q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
-
-    def smqbezier(self, x, y):
-        """smooth quadratic bezier to xy absolut"""
-        self.path.append('T' + str(x) + ',' + str(y))
-
-    def relsmqbezier(self, x, y):
-        """smooth quadratic bezier to xy relative"""
-        self.path.append('t' + str(x) + ',' + str(y))
-
-    def ellarc(self, rx, ry, xrot, laf, sf, x, y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A' + str(rx) + ',' + str(ry) + ' ' + str(xrot) +
-                         ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
-
-    def relellarc(self, rx, ry, xrot, laf, sf, x, y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a' + str(rx) + ',' + str(ry) + ' ' + str(xrot) +
-                         ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
-
-    def __repr__(self):
-        return ' '.join(self.path)
-
-
-class SVGelement:
-
-    """SVGelement(type,attributes,elements,text,namespace,**args)
-    Creates a arbitrary svg element and is intended to be subclassed not used on its own.
-    This element is the base of every svg element it defines a class which resembles
-    a xml-element. The main advantage of this kind of implementation is that you don't
-    have to create a toXML method for every different graph object. Every element
-    consists of a type, attribute, optional subelements, optional text and an optional
-    namespace. Note the elements==None, if elements = None:self.elements=[] construction.
-    This is done because if you default to elements=[] every object has a reference
-    to the same empty list."""
-
-    def __init__(self, type='', attributes=None, elements=None, text='', namespace='', cdata=None, **args):
-        self.type = type
-        if attributes is None:
-            self.attributes = {}
-        else:
-            self.attributes = attributes
-        if elements is None:
-            self.elements = []
-        else:
-            self.elements = elements
-        self.text = text
-        self.namespace = namespace
-        self.cdata = cdata
-        for arg in list(args.keys()):
-            self.attributes[arg] = args[arg]
-
-    def addElement(self, SVGelement):
-        """adds an element to a SVGelement
-
-        SVGelement.addElement(SVGelement)
-        """
-        self.elements.append(SVGelement)
-
-    def toXml(self, level, f):
-        f.write('\t' * level)
-        f.write('<' + self.type)
-        for attkey in list(self.attributes.keys()):
-            f.write(' ' + _escape(str(attkey)) + '=' +
-                    _quoteattr(str(self.attributes[attkey])))
-        if self.namespace:
-            f.write(' xmlns="' + _escape(str(self.namespace)) + '" ')
-            # added by Andreas Heger
-            f.write(
-                ' xmlns:xlink="' + _escape(str("http://www.w3.org/1999/xlink")) + '" ')
-        if self.elements or self.text or self.cdata:
-            f.write('>')
-        if self.elements:
-            f.write('\n')
-        for element in self.elements:
-            element.toXml(level + 1, f)
-        if self.cdata:
-            f.write('\n' + '\t' * (level + 1) + '<![CDATA[')
-            for line in self.cdata.splitlines():
-                f.write('\n' + '\t' * (level + 2) + line)
-            f.write('\n' + '\t' * (level + 1) + ']]>\n')
-        if self.text:
-            if isinstance(self.text, str):  # If the text is only text
-                f.write(_escape(str(self.text)))
-            else:  # If the text is a spannedtext class
-                f.write(str(self.text))
-        if self.elements:
-            f.write('\t' * level + '</' + self.type + '>\n')
-        elif self.text:
-            f.write('</' + self.type + '>\n')
-        elif self.cdata:
-            f.write('\t' * level + '</' + self.type + '>\n')
-        else:
-            f.write('/>\n')
-
-
-class tspan(SVGelement):
-
-    """ts=tspan(text='',**args)
-
-    a tspan element can be used for applying formatting to a textsection
-    usage:
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    st=spannedtext()
-    st.addtspan(ts)
-    t=text(3,5,st)
-    """
-
-    def __init__(self, text=None, **args):
-        SVGelement.__init__(self, 'tspan', **args)
-        if self.text is not None:
-            self.text = text
-
-    def __repr__(self):
-        s = "<tspan"
-        for key, value in list(self.attributes.items()):
-            s += ' %s="%s"' % (key, value)
-        s += '>'
-        s += self.text
-        s += '</tspan>'
-        return s
-
-
-class tref(SVGelement):
-
-    """tr=tref(link='',**args)
-
-    a tref element can be used for referencing text by a link to its id.
-    usage:
-    tr=tref('#linktotext')
-    st=spannedtext()
-    st.addtref(tr)
-    t=text(3,5,st)
-    """
-
-    def __init__(self, link, **args):
-        SVGelement.__init__(self, 'tref', {'xlink:href': link}, **args)
-
-    def __repr__(self):
-        s = "<tref"
-
-        for key, value in list(self.attributes.items()):
-            s += ' %s="%s"' % (key, value)
-        s += '/>'
-        return s
-
-
-class spannedtext:
-
-    """st=spannedtext(textlist=[])
-
-    a spannedtext can be used for text which consists of text, tspan's and tref's
-    You can use it to add to a text element or path element. Don't add it directly
-    to a svg or a group element.
-    usage:
-
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    tr=tref('#linktotext')
-    tr.attributes['fill']='red'
-    st=spannedtext()
-    st.addtspan(ts)
-    st.addtref(tr)
-    st.addtext('This text is not bold')
-    t=text(3,5,st)
-    """
-
-    def __init__(self, textlist=None):
-        if textlist is None:
-            self.textlist = []
-        else:
-            self.textlist = textlist
-
-    def addtext(self, text=''):
-        self.textlist.append(text)
-
-    def addtspan(self, tspan):
-        self.textlist.append(tspan)
-
-    def addtref(self, tref):
-        self.textlist.append(tref)
-
-    def __repr__(self):
-        s = ""
-        for element in self.textlist:
-            s += str(element)
-        return s
-
-
-class rect(SVGelement):
-
-    """r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
-
-    a rectangle is defined by a width and height and a xy pair 
-    """
-
-    def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args):
-        if width is None or height is None:
-            if width is not None:
-                raise ValueError('height is required')
-            if height is not None:
-                raise ValueError('width is required')
-            else:
-                raise ValueError('both height and width are required')
-        SVGelement.__init__(
-            self, 'rect', {'width': width, 'height': height}, **args)
-        if x is not None:
-            self.attributes['x'] = x
-        if y is not None:
-            self.attributes['y'] = y
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-
-
-class ellipse(SVGelement):
-
-    """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
-
-    an ellipse is defined as a center and a x and y radius.
-    """
-
-    def __init__(self, cx=None, cy=None, rx=None, ry=None, fill=None, stroke=None, stroke_width=None, **args):
-        if rx is None or ry is None:
-            if rx is not None:
-                raise ValueError('rx is required')
-            if ry is not None:
-                raise ValueError('ry is required')
-            else:
-                raise ValueError('both rx and ry are required')
-        SVGelement.__init__(self, 'ellipse', {'rx': rx, 'ry': ry}, **args)
-        if cx is not None:
-            self.attributes['cx'] = cx
-        if cy is not None:
-            self.attributes['cy'] = cy
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-
-
-class circle(SVGelement):
-
-    """c=circle(x,y,radius,fill,stroke,stroke_width,**args)
-
-    The circle creates an element using a x, y and radius values eg
-    """
-
-    def __init__(self, cx=None, cy=None, r=None, fill=None, stroke=None, stroke_width=None, **args):
-        if r is None:
-            raise ValueError('r is required')
-        SVGelement.__init__(self, 'circle', {'r': r}, **args)
-        if cx is not None:
-            self.attributes['cx'] = cx
-        if cy is not None:
-            self.attributes['cy'] = cy
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-
-
-class point(circle):
-
-    """p=point(x,y,color)
-
-    A point is defined as a circle with a size 1 radius. It may be more efficient to use a
-    very small rectangle if you use many points because a circle is difficult to render.
-    """
-
-    def __init__(self, x, y, fill='black', **args):
-        circle.__init__(self, x, y, 1, fill, **args)
-
-
-class line(SVGelement):
-
-    """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
-
-    A line is defined by a begin x,y pair and an end x,y pair
-    """
-
-    def __init__(self, x1=None, y1=None, x2=None, y2=None, stroke=None, stroke_width=None, **args):
-        SVGelement.__init__(self, 'line', **args)
-        if x1 is not None:
-            self.attributes['x1'] = x1
-        if y1 is not None:
-            self.attributes['y1'] = y1
-        if x2 is not None:
-            self.attributes['x2'] = x2
-        if y2 is not None:
-            self.attributes['y2'] = y2
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-
-
-class polyline(SVGelement):
-
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
-    a polyline is defined by a list of xy pairs
-    """
-
-    def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
-        SVGelement.__init__(
-            self, 'polyline', {'points': _xypointlist(points)}, **args)
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-
-
-class polygon(SVGelement):
-
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
-    a polygon is defined by a list of xy pairs
-    """
-
-    def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
-        SVGelement.__init__(
-            self, 'polygon', {'points': _xypointlist(points)}, **args)
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-
-
-class path(SVGelement):
-
-    """p=path(path,fill,stroke,stroke_width,**args)
-
-    a path is defined by a path object and optional width, stroke and fillcolor
-    """
-
-    def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None, id=None, **args):
-        SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
-        if stroke is not None:
-            self.attributes['stroke'] = stroke
-        if fill is not None:
-            self.attributes['fill'] = fill
-        if stroke_width is not None:
-            self.attributes['stroke-width'] = stroke_width
-        if id is not None:
-            self.attributes['id'] = id
-
-
-class text(SVGelement):
-
-    """t=text(x,y,text,font_size,font_family,**args)
-
-    a text element can bge used for displaying text on the screen
-    """
-
-    def __init__(self, x=None, y=None, text=None, font_size=None, font_family=None, text_anchor=None, font_style=None, **args):
-        SVGelement.__init__(self, 'text', **args)
-        if x is not None:
-            self.attributes['x'] = x
-        if y is not None:
-            self.attributes['y'] = y
-        if font_size is not None:
-            self.attributes['font-size'] = font_size
-        if font_family is not None:
-            self.attributes['font-family'] = font_family
-        if font_style is not None:
-            self.attributes['font-style'] = font_style
-        if text is not None:
-            self.text = text
-        if text_anchor is not None:
-            self.attributes['text-anchor'] = text_anchor
-
-
-class textpath(SVGelement):
-
-    """tp=textpath(text,link,**args)
-
-    a textpath places a text on a path which is referenced by a link.   
-    """
-
-    def __init__(self, link, text=None, **args):
-        SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args)
-        if text is not None:
-            self.text = text
-
-
-class pattern(SVGelement):
-
-    """p=pattern(x,y,width,height,patternUnits,**args)
-
-    A pattern is used to fill or stroke an object using a pre-defined
-    graphic object which can be replicated ("tiled") at fixed intervals
-    in x and y to cover the areas to be painted.
-    """
-
-    def __init__(self, x=None, y=None, width=None, height=None, patternUnits=None, **args):
-        SVGelement.__init__(self, 'pattern', **args)
-        if x is not None:
-            self.attributes['x'] = x
-        if y is not None:
-            self.attributes['y'] = y
-        if width is not None:
-            self.attributes['width'] = width
-        if height is not None:
-            self.attributes['height'] = height
-        if patternUnits is not None:
-            self.attributes['patternUnits'] = patternUnits
-
-
-class title(SVGelement):
-
-    """t=title(text,**args)
-
-    a title is a text element. The text is displayed in the title bar
-    add at least one to the root svg element
-    """
-
-    def __init__(self, text=None, **args):
-        SVGelement.__init__(self, 'title', **args)
-        if text is not None:
-            self.text = text
-
-
-class description(SVGelement):
-
-    """d=description(text,**args)
-
-    a description can be added to any element and is used for a tooltip
-    Add this element before adding other elements.
-    """
-
-    def __init__(self, text=None, **args):
-        SVGelement.__init__(self, 'desc', **args)
-        if text is not None:
-            self.text = text
-
-
-class lineargradient(SVGelement):
-
-    """lg=lineargradient(x1,y1,x2,y2,id,**args)
-
-    defines a lineargradient using two xy pairs.
-    stop elements van be added to define the gradient colors.
-    """
-
-    def __init__(self, x1=None, y1=None, x2=None, y2=None, id=None, **args):
-        SVGelement.__init__(self, 'linearGradient', **args)
-        if x1 is not None:
-            self.attributes['x1'] = x1
-        if y1 is not None:
-            self.attributes['y1'] = y1
-        if x2 is not None:
-            self.attributes['x2'] = x2
-        if y2 is not None:
-            self.attributes['y2'] = y2
-        if id is not None:
-            self.attributes['id'] = id
-
-
-class radialgradient(SVGelement):
-
-    """rg=radialgradient(cx,cy,r,fx,fy,id,**args)
-
-    defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
-    stop elements van be added to define the gradient colors.
-    """
-
-    def __init__(self, cx=None, cy=None, r=None, fx=None, fy=None, id=None, **args):
-        SVGelement.__init__(self, 'radialGradient', **args)
-        if cx is not None:
-            self.attributes['cx'] = cx
-        if cy is not None:
-            self.attributes['cy'] = cy
-        if r is not None:
-            self.attributes['r'] = r
-        if fx is not None:
-            self.attributes['fx'] = fx
-        if fy is not None:
-            self.attributes['fy'] = fy
-        if id is not None:
-            self.attributes['id'] = id
-
-
-class stop(SVGelement):
-
-    """st=stop(offset,stop_color,**args)
-
-    Puts a stop color at the specified radius
-    """
-
-    def __init__(self, offset, stop_color=None, **args):
-        SVGelement.__init__(self, 'stop', {'offset': offset}, **args)
-        if stop_color is not None:
-            self.attributes['stop-color'] = stop_color
-
-
-class style(SVGelement):
-
-    """st=style(type,cdata=None,**args)
-
-    Add a CDATA element to this element for defing in line stylesheets etc..
-    """
-
-    def __init__(self, type, cdata=None, **args):
-        SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args)
-
-
-class image(SVGelement):
-
-    """im=image(url,width,height,x,y,**args)
-
-    adds an image to the drawing. Supported formats are .png, .jpg and .svg.
-    """
-
-    def __init__(self, url, x=None, y=None, width=None, height=None, **args):
-        if width is None or height is None:
-            if width is not None:
-                raise ValueError('height is required')
-            if height is not None:
-                raise ValueError('width is required')
-            else:
-                raise ValueError('both height and width are required')
-        SVGelement.__init__(
-            self, 'image', {'xlink:href': url, 'width': width, 'height': height}, **args)
-        if x is not None:
-            self.attributes['x'] = x
-        if y is not None:
-            self.attributes['y'] = y
-
-
-class cursor(SVGelement):
-
-    """c=cursor(url,**args)
-
-    defines a custom cursor for a element or a drawing
-    """
-
-    def __init__(self, url, **args):
-        SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args)
-
-
-class marker(SVGelement):
-
-    """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
-
-    defines a marker which can be used as an endpoint for a line or other pathtypes
-    add an element to it which should be used as a marker.
-    """
-
-    def __init__(self, id=None, viewBox=None, refx=None, refy=None, markerWidth=None, markerHeight=None, **args):
-        SVGelement.__init__(self, 'marker', **args)
-        if id is not None:
-            self.attributes['id'] = id
-        if viewBox is not None:
-            self.attributes['viewBox'] = _viewboxlist(viewBox)
-        if refx is not None:
-            self.attributes['refX'] = refx
-        if refy is not None:
-            self.attributes['refY'] = refy
-        if markerWidth is not None:
-            self.attributes['markerWidth'] = markerWidth
-        if markerHeight is not None:
-            self.attributes['markerHeight'] = markerHeight
-
-
-class group(SVGelement):
-
-    """g=group(id,**args)
-
-    a group is defined by an id and is used to contain elements
-    g.addElement(SVGelement)
-    """
-
-    def __init__(self, id=None, **args):
-        SVGelement.__init__(self, 'g', **args)
-        if id is not None:
-            self.attributes['id'] = id
-
-
-class symbol(SVGelement):
-
-    """sy=symbol(id,viewbox,**args)
-
-    defines a symbol which can be used on different places in your graph using
-    the use element. A symbol is not rendered but you can use 'use' elements to
-    display it by referencing its id.
-    sy.addElement(SVGelement)
-    """
-
-    def __init__(self, id=None, viewBox=None, **args):
-        SVGelement.__init__(self, 'symbol', **args)
-        if id is not None:
-            self.attributes['id'] = id
-        if viewBox is not None:
-            self.attributes['viewBox'] = _viewboxlist(viewBox)
-
-
-class defs(SVGelement):
-
-    """d=defs(``**args``)
-
-    container for defining elements
-    """
-
-    def __init__(self, **args):
-        SVGelement.__init__(self, 'defs', **args)
-
-
-class switch(SVGelement):
-
-    """sw=switch(``**args``)
-
-    Elements added to a switch element which are "switched" by the attributes
-    requiredFeatures, requiredExtensions and systemLanguage.
-    Refer to the SVG specification for details.
-    """
-
-    def __init__(self, **args):
-        SVGelement.__init__(self, 'switch', **args)
-
-
-class use(SVGelement):
-
-    """u=use(link,x,y,width,height,``**args``)
-
-    references a symbol by linking to its id and its position, height and width
-    """
-
-    def __init__(self, link, x=None, y=None, width=None, height=None, **args):
-        SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
-        if x is not None:
-            self.attributes['x'] = x
-        if y is not None:
-            self.attributes['y'] = y
-
-        if width is not None:
-            self.attributes['width'] = width
-        if height is not None:
-            self.attributes['height'] = height
-
-
-class link(SVGelement):
-
-    """a=link(url,``**args``)
-
-    a link  is defined by a hyperlink. add elements which have to be linked
-    a.addElement(SVGelement)
-    """
-
-    def __init__(self, link='', **args):
-        SVGelement.__init__(self, 'a', {'xlink:href': link}, **args)
-
-
-class view(SVGelement):
-
-    """v=view(id,``**args``)
-
-    a view can be used to create a view with different attributes"""
-
-    def __init__(self, id=None, **args):
-        SVGelement.__init__(self, 'view', **args)
-        if id is not None:
-            self.attributes['id'] = id
-
-
-class script(SVGelement):
-
-    """sc=script(type,type,cdata,``**args``)
-
-    adds a script element which contains CDATA to the SVG drawing
-
-    """
-
-    def __init__(self, type, cdata=None, **args):
-        SVGelement.__init__(
-            self, 'script', {'type': type}, cdata=cdata, **args)
-
-
-class animate(SVGelement):
-
-    """an=animate(attribute,from,to,during,``**args``)
-
-    animates an attribute.    
-    """
-
-    def __init__(self, attribute, fr=None, to=None, dur=None, **args):
-        SVGelement.__init__(
-            self, 'animate', {'attributeName': attribute}, **args)
-        if fr is not None:
-            self.attributes['from'] = fr
-        if to is not None:
-            self.attributes['to'] = to
-        if dur is not None:
-            self.attributes['dur'] = dur
-
-
-class animateMotion(SVGelement):
-
-    """an=animateMotion(pathdata,dur,``**args``)
-
-    animates a SVGelement over the given path in dur seconds
-    """
-
-    def __init__(self, pathdata, dur, **args):
-        SVGelement.__init__(self, 'animateMotion', **args)
-        if pathdata is not None:
-            self.attributes['path'] = str(pathdata)
-        if dur is not None:
-            self.attributes['dur'] = dur
-
-
-class animateTransform(SVGelement):
-
-    """antr=animateTransform(type,from,to,dur,``**args``)
-
-    transform an element from and to a value.
-    """
-
-    def __init__(self, type=None, fr=None, to=None, dur=None, **args):
-        SVGelement.__init__(
-            self, 'animateTransform', {'attributeName': 'transform'}, **args)
-        # As far as I know the attributeName is always transform
-        if type is not None:
-            self.attributes['type'] = type
-        if fr is not None:
-            self.attributes['from'] = fr
-        if to is not None:
-            self.attributes['to'] = to
-        if dur is not None:
-            self.attributes['dur'] = dur
-
-
-class animateColor(SVGelement):
-
-    """ac=animateColor(attribute,type,from,to,dur,``**args``)
-
-    Animates the color of a element
-    """
-
-    def __init__(self, attribute, type=None, fr=None, to=None, dur=None, **args):
-        SVGelement.__init__(
-            self, 'animateColor', {'attributeName': attribute}, **args)
-        if type is not None:
-            self.attributes['type'] = type
-        if fr is not None:
-            self.attributes['from'] = fr
-        if to is not None:
-            self.attributes['to'] = to
-        if dur is not None:
-            self.attributes['dur'] = dur
-
-
-class set(SVGelement):
-
-    """st=set(attribute,to,during,``**args``)
-
-    sets an attribute to a value for a
-    """
-
-    def __init__(self, attribute, to=None, dur=None, **args):
-        SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args)
-        if to is not None:
-            self.attributes['to'] = to
-        if dur is not None:
-            self.attributes['dur'] = dur
-
-
-class svg(SVGelement):
-
-    """s=svg(viewbox,width,height,``**args``)
-
-    a svg or element is the root of a drawing add all elements to a svg element.
-    You can have different svg elements in one svg file
-    s.addElement(SVGelement)
-
-    eg
-    d=drawing()
-    s=svg((0,0,100,100),'100%','100%')
-    c=circle(50,50,20)
-    s.addElement(c)
-    d.setSVG(s)
-    d.toXml()
-    """
-
-    def __init__(self, viewBox=None, width=None, height=None, **args):
-        SVGelement.__init__(self, 'svg', **args)
-        if viewBox is not None:
-            self.attributes['viewBox'] = _viewboxlist(viewBox)
-        if width is not None:
-            self.attributes['width'] = width
-        if height is not None:
-            self.attributes['height'] = height
-        self.namespace = "http://www.w3.org/2000/svg"
-
-
-class drawing:
-
-    """d=drawing()
-
-    this is the actual SVG document. It needs a svg element as a root.
-    Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG
-    source to the screen or to a file
-    d=drawing()
-    d.addSVG(svg)
-    d.toXml(optionalfilename)
-    """
-
-    def __init__(self):
-        self.svg = None
-
-    def setSVG(self, svg):
-        self.svg = svg
-        # Voeg een element toe aan de grafiek toe.
-    if use_dom_implementation == 0:
-        def toXml(self, filename='', compress=False):
-            xml = StringIO()
-            xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
-            xml.write(
-                "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd \">\n")
-            self.svg.toXml(0, xml)
-            if not filename:
-                if compress:
-                    import gzip
-                    f = StringIO()
-                    zf = gzip.GzipFile(fileobj=f, mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                if filename[-4:] == 'svgz':
-                    import gzip
-                    f = gzip.GzipFile(
-                        filename=filename, mode="wb", compresslevel=9)
-                    f.write(xml.getvalue())
-                    f.close()
-                else:
-                    f = file(filename, 'w')
-                    f.write(xml.getvalue())
-                    f.close()
-
-    else:
-        def toXml(self, filename='', compress=False):
-            """drawing.toXml()        ---->to the screen
-            drawing.toXml(filename)---->to the file
-            writes a svg drawing to the screen or to a file
-            compresses if filename ends with svgz or if compress is true
-            """
-            doctype = implementation.createDocumentType(
-                'svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
-
-            global root
-            # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
-            # that is a bit messy.
-            root = implementation.createDocument(None, None, doctype)
-            # Create the xml document.
-            global appender
-
-            def appender(element, elementroot):
-                """This recursive function appends elements to an element and sets the attributes
-                and type. It stops when alle elements have been appended"""
-                if element.namespace:
-                    e = root.createElementNS(element.namespace, element.type)
-                else:
-                    e = root.createElement(element.type)
-                if element.text:
-                    textnode = root.createTextNode(element.text)
-                    e.appendChild(textnode)
-                # in element.attributes is supported from python 2.2
-                for attribute in list(element.attributes.keys()):
-                    e.setAttribute(
-                        attribute, str(element.attributes[attribute]))
-                if element.elements:
-                    for el in element.elements:
-                        e = appender(el, e)
-                elementroot.appendChild(e)
-                return elementroot
-            root = appender(self.svg, root)
-            if not filename:
-                xml = StringIO()
-                PrettyPrint(root, xml)
-                if compress:
-                    import gzip
-                    f = StringIO()
-                    zf = gzip.GzipFile(fileobj=f, mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                try:
-                    if filename[-4:] == 'svgz':
-                        import gzip
-                        xml = StringIO()
-                        PrettyPrint(root, xml)
-                        f = gzip.GzipFile(
-                            filename=filename, mode='wb', compresslevel=9)
-                        f.write(xml.getvalue())
-                        f.close()
-                    else:
-                        f = open(filename, 'w')
-                        PrettyPrint(root, f)
-                        f.close()
-                except:
-                    print("Cannot write SVG file: " + filename)
-
-    def validate(self):
-        try:
-            import xml.parsers.xmlproc.xmlval
-        except:
-            raise ImportError('PyXml is required for validating SVG')
-        svg = self.toXml()
-        xv = xml.parsers.xmlproc.xmlval.XMLValidator()
-        try:
-            xv.feed(svg)
-        except:
-            raise ValueError("SVG is not well formed, see messages above")
-        else:
-            print("SVG well formed")
-
-
-if __name__ == '__main__':
-
-    d = drawing()
-    s = svg((0, 0, 100, 100))
-    r = rect(-100, -100, 300, 300, 'cyan')
-    s.addElement(r)
-
-    t = title('SVGdraw Demo')
-    s.addElement(t)
-    g = group('animations')
-    e = ellipse(0, 0, 5, 2)
-    g.addElement(e)
-    c = circle(0, 0, 1, 'red')
-    g.addElement(c)
-    pd = pathdata(0, -10)
-    for i in range(6):
-        pd.relsmbezier(10, 5, 0, 10)
-        pd.relsmbezier(-10, 5, 0, 10)
-    an = animateMotion(pd, 10)
-    an.attributes['rotate'] = 'auto-reverse'
-    an.attributes['repeatCount'] = "indefinite"
-    g.addElement(an)
-    s.addElement(g)
-    for i in range(20, 120, 20):
-        u = use('#animations', i, 0)
-        s.addElement(u)
-    for i in range(0, 120, 20):
-        for j in range(5, 105, 10):
-            c = circle(i, j, 1, 'red', 'black', .5)
-            s.addElement(c)
-    d.setSVG(s)
-
-    print(d.toXml())
diff --git a/cgat/tools/gff2gff.py b/cgat/tools/gff2gff.py
index d44a8e6af..426773e79 100644
--- a/cgat/tools/gff2gff.py
+++ b/cgat/tools/gff2gff.py
@@ -3,6 +3,8 @@
 
 :Tags: Genomics Intervals GFF Manipulation
 
+Note: The script can parse AGP files but this functionality
+is scheduled for deprecation in the next release.
 
 Purpose
 -------
diff --git a/cgat/version.py b/cgat/version.py
index 49e0fc1e0..a5f830a2c 100644
--- a/cgat/version.py
+++ b/cgat/version.py
@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.1"
diff --git a/dependency_graph/Makefile b/dependency_graph/Makefile
deleted file mode 100644
index 10856d2ab..000000000
--- a/dependency_graph/Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-NAME = cgat
-ROOT = ../scripts ../CGAT ../../CGATPipelines/CGATPipelines
-PDFS = $(NAME)_raw.pdf 
-SVGS = $(NAME)_raw.svg
-CHECK = $(NAME).check
-
-
-FOOD_FLAGS?=--internal --follow
-
-.SUFFIXES: .deps .dot .pdf .svg .clusters
-
-all: $(PDFS) $(SVGS)
-
-check: $(CHECK)
-
-raw.deps: $(ROOT)
-	sfood $(FOOD_FLAGS) $(ROOT) > $@
-
-$(NAME).clusters: $(ROOT)
-	cd $(ROOT) ; ls -1d * > $(shell pwd)/$@
-
-$(NAME).deps: $(NAME).clusters raw.deps
-	cat raw.deps | sfood-cluster -f $< > $@
-
-$(NAME)_raw.deps: raw.deps
-	cp $< $@
-
-.deps.pdf:
-	cat $< | python graph.py | dot -Tps | ps2pdf - $@
-
-.deps.svg:
-	cat $< | python graph.py | dot -Tsvg > $@
-
-$(NAME).check:
-	sfood-checker $(ROOT) >& $@
-
-clean:
-	rm -f *.clusters *.dot *.pdf *.svg
-	ls -1 *.deps | grep -v ^raw.deps | xargs rm -f
-
-realclean: clean
-	rm -f raw.deps
diff --git a/dependency_graph/cgat_raw.svg b/dependency_graph/cgat_raw.svg
deleted file mode 100644
index 53ba6e9c1..000000000
--- a/dependency_graph/cgat_raw.svg
+++ /dev/null
@@ -1,8203 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
- "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
- -->
-<!-- Title: dependencies Pages: 1 -->
-<svg width="575pt" height="720pt"
- viewBox="0.00 0.00 575.07 720.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(0.0287455 0.0287455) rotate(0) translate(4 25043.4)">
-<title>dependencies</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-25043.4 20001.5,-25043.4 20001.5,4 -4,4"/>
-<!-- CGATPipelines -->
-<g id="node1" class="node"><title>CGATPipelines</title>
-<ellipse fill="#999999" stroke="#999999" cx="9213.54" cy="-15266.4" rx="48.9176" ry="18"/>
-<text text-anchor="middle" x="9213.54" y="-15263.4" font-family="Times,serif" font-size="10.00">CGATPipelines</text>
-</g>
-<!-- CGATPipelines/Pipeline -->
-<g id="node2" class="node"><title>CGATPipelines/Pipeline</title>
-<ellipse fill="#e69f00" stroke="#e69f00" cx="9213.54" cy="-4045.36" rx="70.2133" ry="18"/>
-<text text-anchor="middle" x="9213.54" y="-4042.36" font-family="Times,serif" font-size="10.00">CGATPipelines/Pipeline</text>
-</g>
-<!-- CGATPipelines/Pipeline/Control.py -->
-<g id="node3" class="node"><title>CGATPipelines/Pipeline/Control.py</title>
-<ellipse fill="#56b4e9" stroke="#56b4e9" cx="10552.5" cy="-2445.36" rx="98.0361" ry="18"/>
-<text text-anchor="middle" x="10552.5" y="-2442.36" font-family="Times,serif" font-size="10.00">CGATPipelines/Pipeline/Control.py</text>
-</g>
-<!-- CGATPipelines/Pipeline&#45;&gt;CGATPipelines/Pipeline/Control.py -->
-<g id="edge1" class="edge"><title>CGATPipelines/Pipeline&#45;&gt;CGATPipelines/Pipeline/Control.py</title>
-<path fill="none" stroke="black" d="M9221.52,-4027.22C9278.57,-3881.57 9683.47,-2897.25 10363.1,-2477.36 10387.5,-2462.31 10416.8,-2453.77 10445.1,-2449.06"/>
-<polygon fill="black" stroke="black" points="10445.6,-2452.52 10455,-2447.55 10444.6,-2445.6 10445.6,-2452.52"/>
-</g>
-<!-- CGATPipelines/Pipeline/Database.py -->
-<g id="node4" class="node"><title>CGATPipelines/Pipeline/Database.py</title>
-<ellipse fill="#56b4e9" stroke="#56b4e9" cx="10552.5" cy="-2391.36" rx="102.455" ry="18"/>
-<text text-anchor="middle" x="10552.5" y="-2388.36" font-family="Times,serif" font-size="10.00">CGATPipelines/Pipeline/Database.py</text>
-</g>
-<!-- CGATPipelines/Pipeline&#45;&gt;CGATPipelines/Pipeline/Database.py -->
-<g id="edge2" class="edge"><title>CGATPipelines/Pipeline&#45;&gt;CGATPipelines/Pipeline/Database.py</title>
-<path fill="none" stroke="black" d="M9220.87,-4027.35C9274.14,-3878.49 9663.45,-2846.58 10363.1,-2418.36 10386,-2404.37 10413.3,-2396.53 10439.9,-2392.36"/>
-<polygon fill="black" stroke="black" points="10440.7,-2395.79 10450.1,-2390.93 10439.7,-2388.85 10440.7,-2395.79"/>
-</g>
-<!-- CGATPipelines/Pipeline/Execution.py -->
-<g id="node5" class="node"><title>CGATPipelines/Pipeline/Execution.py</title>
-<ellipse fill="#56b4e9" stroke="#56b4e9" cx="12292.5" cy="-2309.36" rx="104.063" ry="18"/>
-<text text-anchor="middle" x="12292.5" y="-2306.36" font-family="Times,serif" font-size="10.00">CGATPipelines/Pipeline/Execution.py</text>
-</g>
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-</g>
-<!-- scripts/transfac2transfac.py&#45;&gt;CGAT/Experiment.py -->
-<g id="edge1144" class="edge"><title>scripts/transfac2transfac.py&#45;&gt;CGAT/Experiment.py</title>
-<path fill="none" stroke="black" d="M14135.5,-5581.13C14175.1,-5582.6 14222.7,-5590.81 14256.6,-5617.36 15599.8,-6669.82 15838.3,-9060.72 15862.3,-9347.96"/>
-<polygon fill="black" stroke="black" points="15858.9,-9348.66 15863.2,-9358.34 15865.8,-9348.09 15858.9,-9348.66"/>
-</g>
-<!-- scripts/vcf2vcf.py -->
-<g id="node481" class="node"><title>scripts/vcf2vcf.py</title>
-<ellipse fill="#cc79a7" stroke="#cc79a7" cx="7652.54" cy="-8149.36" rx="53.5381" ry="18"/>
-<text text-anchor="middle" x="7652.54" y="-8146.36" font-family="Times,serif" font-size="10.00">scripts/vcf2vcf.py</text>
-</g>
-<!-- scripts/vcf2vcf.py&#45;&gt;CGAT/Experiment.py -->
-<g id="edge1145" class="edge"><title>scripts/vcf2vcf.py&#45;&gt;CGAT/Experiment.py</title>
-<path fill="none" stroke="black" d="M7706.01,-8147.15C7758.88,-8142.39 7840.26,-8127.91 7894.88,-8084.36 8802.54,-7360.82 8132.8,-6389.34 9119.13,-5777.36 9272.41,-5682.26 10563.3,-5756.94 10742,-5732.36 11359.5,-5647.44 11488.4,-5498.44 12102.5,-5391.36 12269.8,-5362.21 12316,-5386.1 12482.6,-5353.36 13111.2,-5229.83 13230.5,-5035.43 13864.5,-4943.36 14037,-4918.32 14113.9,-4843.34 14256.6,-4943.36 15071.6,-5514.75 15789.1,-9000.44 15859,-9348.38"/>
-<polygon fill="black" stroke="black" points="15855.6,-9349.27 15861,-9358.39 15862.4,-9347.9 15855.6,-9349.27"/>
-</g>
-<!-- scripts/vcf2vcf.py&#45;&gt;CGAT/VCF.py -->
-<g id="edge1146" class="edge"><title>scripts/vcf2vcf.py&#45;&gt;CGAT/VCF.py</title>
-<path fill="none" stroke="black" d="M7702.85,-8143.09C7754.65,-8139.04 7836.54,-8140.05 7894.88,-8176.36 8743.68,-8704.61 9145.64,-10004.1 9204.81,-10209.8"/>
-<polygon fill="black" stroke="black" points="9201.48,-10210.8 9207.59,-10219.5 9208.21,-10208.9 9201.48,-10210.8"/>
-</g>
-<!-- scripts/vcfstats2db.py -->
-<g id="node482" class="node"><title>scripts/vcfstats2db.py</title>
-<ellipse fill="#cc79a7" stroke="#cc79a7" cx="14060.5" cy="-4001.36" rx="62.5783" ry="18"/>
-<text text-anchor="middle" x="14060.5" y="-3998.36" font-family="Times,serif" font-size="10.00">scripts/vcfstats2db.py</text>
-</g>
-<!-- scripts/vcfstats2db.py&#45;&gt;CGAT/Experiment.py -->
-<g id="edge1147" class="edge"><title>scripts/vcfstats2db.py&#45;&gt;CGAT/Experiment.py</title>
-<path fill="none" stroke="black" d="M14118.1,-3994.03C14161,-3991.72 14218.8,-3996.01 14256.6,-4028.36 15155.6,-4798.19 15802.4,-8964.08 15860.3,-9348.01"/>
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-<!-- scripts/vcfstats2db.py&#45;&gt;CGAT/IOTools.py -->
-<g id="edge1148" class="edge"><title>scripts/vcfstats2db.py&#45;&gt;CGAT/IOTools.py</title>
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-<polygon fill="black" stroke="black" points="17720.3,-7544.07 17727,-7552.25 17726.8,-7541.65 17720.3,-7544.07"/>
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-<!-- scripts/version.py -->
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-<ellipse fill="#cc79a7" stroke="#cc79a7" cx="951.544" cy="-25021.4" rx="52.8356" ry="18"/>
-<text text-anchor="middle" x="951.544" y="-25018.4" font-family="Times,serif" font-size="10.00">scripts/version.py</text>
-</g>
-<!-- scripts/wig2bed.py -->
-<g id="node484" class="node"><title>scripts/wig2bed.py</title>
-<ellipse fill="#cc79a7" stroke="#cc79a7" cx="12292.5" cy="-16197.4" rx="55.8489" ry="18"/>
-<text text-anchor="middle" x="12292.5" y="-16194.4" font-family="Times,serif" font-size="10.00">scripts/wig2bed.py</text>
-</g>
-<!-- scripts/wig2bed.py&#45;&gt;CGAT/Experiment.py -->
-<g id="edge1149" class="edge"><title>scripts/wig2bed.py&#45;&gt;CGAT/Experiment.py</title>
-<path fill="none" stroke="black" d="M12344.8,-16203.8C12386.6,-16206.2 12444.7,-16202.3 12482.6,-16170.4 14019.9,-14872.3 12312.7,-13140 13864.5,-11859.4 13999.9,-11747.7 14107.3,-11904.6 14256.6,-11812.4 15278.3,-11181.2 15786.3,-9631.01 15856.2,-9404.23"/>
-<polygon fill="black" stroke="black" points="15859.6,-9405.03 15859.2,-9394.44 15852.9,-9402.98 15859.6,-9405.03"/>
-</g>
-<!-- scripts/wig2bed.py&#45;&gt;CGAT/IOTools.py -->
-<g id="edge1150" class="edge"><title>scripts/wig2bed.py&#45;&gt;CGAT/IOTools.py</title>
-<path fill="none" stroke="black" d="M12344,-16204.5C12382.2,-16210.3 12435.9,-16219.1 12482.6,-16229.4 13104.3,-16366.7 13233.4,-16522.6 13864.5,-16607.4 13948.4,-16618.6 16010,-16621.6 16064.6,-16575.4 17562.7,-15306.8 17723.5,-8107.37 17733,-7598.71"/>
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-</g>
-<!-- scripts/wig2bed.py&#45;&gt;CGAT/IndexedFasta.py -->
-<g id="edge1151" class="edge"><title>scripts/wig2bed.py&#45;&gt;CGAT/IndexedFasta.py</title>
-<path fill="none" stroke="black" d="M12306.9,-16215.1C12339.8,-16259.6 12426.7,-16380.3 12482.6,-16490.4 13258.1,-18017.8 13078,-18566.6 13864.5,-20088.4 13918.6,-20193.1 14001.9,-20306.3 14039.7,-20355.8"/>
-<polygon fill="black" stroke="black" points="14036.9,-20357.9 14045.8,-20363.7 14042.4,-20353.7 14036.9,-20357.9"/>
-</g>
-<!-- scripts/wig2wig.py -->
-<g id="node485" class="node"><title>scripts/wig2wig.py</title>
-<ellipse fill="#cc79a7" stroke="#cc79a7" cx="12292.5" cy="-15301.4" rx="55.8489" ry="18"/>
-<text text-anchor="middle" x="12292.5" y="-15298.4" font-family="Times,serif" font-size="10.00">scripts/wig2wig.py</text>
-</g>
-<!-- scripts/wig2wig.py&#45;&gt;CGAT/Experiment.py -->
-<g id="edge1152" class="edge"><title>scripts/wig2wig.py&#45;&gt;CGAT/Experiment.py</title>
-<path fill="none" stroke="black" d="M12333,-15288.9C12375.3,-15273.7 12441.7,-15244.2 12482.6,-15198.4 13572.3,-13976.3 12563.8,-12777.9 13864.5,-11783.4 14003.9,-11676.8 14106.6,-11827.5 14256.6,-11736.4 15259.7,-11126.9 15782.6,-9626.38 15855.6,-9404.07"/>
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-<!-- scripts/wig2wig.py&#45;&gt;CGAT/IndexedFasta.py -->
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diff --git a/dependency_graph/graph.py b/dependency_graph/graph.py
deleted file mode 100644
index 815d76715..000000000
--- a/dependency_graph/graph.py
+++ /dev/null
@@ -1,116 +0,0 @@
-"""
-Read snakefood dependencies and output a visual graph.
-"""
-# This file is part of the Snakefood open source package.
-# See http://furius.ca/snakefood/ for licensing details.
-
-# Modified by AH to colour nodes according to subdir.
-
-import sys
-import os
-
-from snakefood.depends import read_depends, eliminate_redundant_depends
-
-prefix = '''
-# This file was generated by sfood-graph.
-
-strict digraph "dependencies" {
-    graph [
-        rankdir = "LR",
-        overlap = "scale",
-        size = "8,10",
-        ratio = "fill",
-        fontsize = "16",
-        fontname = "Helvetica",
-        clusterrank = "local"
-        ]
-
-       node [
-           fontsize=%s
-           shape=ellipse
-           // style=filled
-           // shape=box
-       ];
-
-'''
-postfix = '''
-
-}
-'''
-
-COLORS = ["#999999", "#E69F00", "#56B4E9", "#009E73",
-          "#F0E442", "#0072B2", "#D55E00", "#CC79A7"]
-
-
-def graph(pairs, write, fontsize, color_map):
-    "Given (from, to) pairs of (root, fn) files, output a dot graph."
-    write(prefix % fontsize)
-    for (froot, f), (troot, t) in pairs:
-        if opts.pythonify_filenames:
-            f = normpyfn(f)
-            t = normpyfn(t)
-        if opts.full_pathnames:
-            f = os.path.join(froot, f)
-            if troot:
-                t = os.path.join(troot, t)
-        if troot is None:
-            dn = os.path.dirname(f)
-            if dn not in color_map:
-                color_map[dn] = COLORS[len(color_map) % len(COLORS)]
-            write('"%s"  [style=filled, color="%s"];\n' % (f, color_map[dn]))
-        else:
-            write('"%s" -> "%s";\n' % (f, t))
-    write(postfix)
-
-
-def normpyfn(fn):
-    "Normalize the python filenames for output."
-    if fn is None:
-        return fn
-    if fn.endswith('.py'):
-        fn = fn[:-3]
-    fn = fn.replace(os.sep, '.')
-    return fn
-
-
-def main():
-    import optparse
-    parser = optparse.OptionParser(__doc__.strip())
-
-    parser.add_option('-f', '--full-pathnames', '--full', action='store_true',
-                      help="Output the full pathnames, not just the relative.")
-
-    parser.add_option('-p', '--pythonify-filenames', '--remove-extensions',
-                      action='store_true',
-                      help="Remove filename extensions in the graph and "
-                      "replace slashes with dots.")
-
-    parser.add_option('-r', '--redundant', action='store_false', default=True,
-                      help="Do not eliminate redundant dependencies.")
-
-    parser.add_option('--fontsize', action='store', type='int',
-                      default=10,
-                      help="The size of the font to use for nodes.")
-
-    global opts
-    opts, args = parser.parse_args()
-
-    if not args:
-        args = ['-']
-
-    color_map = {}
-
-    for fn in args:
-        if fn == '-':
-            f = sys.stdin
-        else:
-            f = open(fn)
-        depends = read_depends(f)
-        if opts.redundant:
-            depends = eliminate_redundant_depends(depends)
-        graph(depends, sys.stdout.write, opts.fontsize, color_map)
-
-
-if __name__ == "__main__":
-    main()
-
diff --git a/deprecated_scripts.md b/deprecated_scripts.md
new file mode 100644
index 000000000..19051fcc8
--- /dev/null
+++ b/deprecated_scripts.md
@@ -0,0 +1,22 @@
+#Scripts that have been deprecated:
+chain2psl
+bam2UniquePairs
+bam2libtype
+bam2peakshape
+bed2annotator
+bed2plot
+cat_tables
+cgat_fasta2cDNA
+combine_tables
+csv_interestion
+csv_rename
+csv_select
+csv_set
+medip_merge_intervals
+rndomize_lines
+transfac2transfac
+
+# Warnings for deprecation in the next release
+AGP.py (its used once in gff2gff to parse agp files)
+Blat.py
+gff2psl
\ No newline at end of file
diff --git a/install.sh b/install.sh
deleted file mode 100755
index 55572178f..000000000
--- a/install.sh
+++ /dev/null
@@ -1,966 +0,0 @@
-#!/usr/bin/env bash
-
-# References
-# http://kvz.io/blog/2013/11/21/bash-best-practices/
-# http://jvns.ca/blog/2017/03/26/bash-quirks/
-
-# exit when a command fails
-set -o errexit
-
-# exit if any pipe commands fail
-set -o pipefail
-
-# exit when your script tries to use undeclared variables
-#set -o nounset
-
-# trace what gets executed
-#set -o xtrace
-
-# Bash traps
-# http://aplawrence.com/Basics/trapping_errors.html
-# https://stelfox.net/blog/2013/11/fail-fast-in-bash-scripts/
-
-set -o errtrace
-
-SCRIPT_NAME="$0"
-SCRIPT_PARAMS="$@"
-
-error_handler() {
-   echo
-   echo " ########################################################## "
-   echo
-   echo " An error occurred in:"
-   echo
-   echo " - line number: ${1}"
-   shift
-   echo " - exit status: ${1}"
-   shift
-   echo " - command: ${@}"
-   echo
-   echo " The script will abort now. User input was: "
-   echo
-   echo " ${SCRIPT_NAME} ${SCRIPT_PARAMS}"
-   echo
-   echo " Please copy and paste this error and report it via Git Hub: "
-   echo " https://github.com/cgat-developers/cgat-apps/issues "
-   print_env_vars
-   echo " ########################################################## "
-}
-
-trap 'error_handler ${LINENO} $? ${BASH_COMMAND}' ERR INT TERM
-
-# log installation information
-log() {
-   echo "# install.sh log | `hostname` | `date` | $1 "
-}
-
-# report error and exit
-report_error() {
-   echo
-   echo $1
-   echo
-   echo "Aborting."
-   echo
-   exit 1
-}
-
-# detect CGAT installation
-detect_cgat_installation() {
-
-if [[ -z "$CGAT_HOME" ]] ; then
-
-   if [[ -d "$HOME/cgat-install/conda-install" ]] ; then
-      UNINSTALL_DIR="$HOME/cgat-install"
-   fi
-
-else
-
-   if [[ -d "$CGAT_HOME/conda-install" ]] ; then
-      UNINSTALL_DIR="$CGAT_HOME"
-   fi
-
-fi
-
-} # detect_cgat_installation
-
-
-# configure environment variables
-# set: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_APPS
-get_cgat_env() {
-
-if [[ $TRAVIS_INSTALL ]] ; then
-
-   CGAT_HOME=$TRAVIS_BUILD_DIR
-   CONDA_INSTALL_TYPE_APPS="cgat-apps.yml"
-   CONDA_INSTALL_TYPE_CORE="cgat-core.yml"
-
-elif [[ $JENKINS_INSTALL ]] ; then
-
-   CGAT_HOME=$WORKSPACE
-   CONDA_INSTALL_TYPE_APPS="cgat-apps.yml"
-   CONDA_INSTALL_TYPE_CORE="cgat-core.yml"
-
-else
-
-   if [[ -z $CGAT_HOME  ]] ; then
-      CGAT_HOME=$HOME/cgat-install
-   fi
-
-   if [[ $INSTALL_PRODUCTION ]] ; then
-      CONDA_INSTALL_TYPE_APPS="cgat-apps.yml"
-      CONDA_INSTALL_TYPE_CORE="cgat-core.yml"
-   elif [[ $INSTALL_DEVEL ]] ; then
-      CONDA_INSTALL_TYPE_APPS="cgat-apps.yml"
-      CONDA_INSTALL_TYPE_CORE="cgat-core.yml"
-   elif [[ $INSTALL_TEST ]] || [[ $INSTALL_UPDATE ]] ; then
-      if [[ -d $CGAT_HOME/conda-install ]] ; then
-         AUX=`find $CGAT_HOME/conda-install/envs/cgat-* -maxdepth 0`
-	 CONDA_INSTALL_TYPE_APPS=`basename $AUX`
-      else
-         echo
-         echo " The location of the CGAT code was not found (function: get_cgat_env). "
-	 echo " Please install it first or use --location option with full path to your installation. "
-         echo
-         exit 1
-      fi
-   else
-      echo
-      echo " Wrong installation type! "
-      echo " Installation aborted. "
-      echo
-      exit 1
-   fi # if install type
-
-fi # if travis install
-
-CONDA_INSTALL_DIR=$CGAT_HOME/conda-install
-
-# set conda environment name
-[[ ${CONDA_INSTALL_ENV} ]] || CONDA_INSTALL_ENV="cgat-a"
-
-} # get_cgat_env
-
-
-# setup environment variables
-setup_env_vars() {
-
-export CFLAGS=$CFLAGS" -I$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include -L$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib"
-export CPATH=$CPATH" -I$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include -L$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib"
-export C_INCLUDE_PATH=$C_INCLUDE_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include
-export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include
-export LIBRARY_PATH=$LIBRARY_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib/R/lib
-
-} # setup_env_vars
-
-# print related environment variables
-print_env_vars() {
-
-echo
-echo " Debugging: "
-echo " CFLAGS: "$CFLAGS
-echo " CPATH: "$CPATH
-echo " C_INCLUDE_PATH: "$C_INCLUDE_PATH
-echo " CPLUS_INCLUDE_PATH: "$CPLUS_INCLUDE_PATH
-echo " LIBRARY_PATH: "$LIBRARY_PATH
-echo " LD_LIBRARY_PATH: "$LD_LIBRARY_PATH
-echo " CGAT_HOME: "$CGAT_HOME
-echo " CONDA_INSTALL_DIR: "$CONDA_INSTALL_DIR
-echo " CONDA_INSTALL_TYPE_APPS: "$CONDA_INSTALL_TYPE_APPS
-echo " CONDA_INSTALL_TYPE_CORE: "$CONDA_INSTALL_TYPE_CORE
-echo " CONDA_INSTALL_ENV: "$CONDA_INSTALL_ENV
-echo " PYTHONPATH: "$PYTHONPATH
-[[ ! $INSTALL_TEST ]] && echo " INSTALL_BRANCH: "$INSTALL_BRANCH
-[[ ! $INSTALL_TEST ]] && echo " CORE_BRANCH: "$CORE_BRANCH
-[[ ! $INSTALL_TEST ]] && echo " RELEASE: "$RELEASE
-[[ ! $INSTALL_TEST ]] && echo " CODE_DOWNLOAD_TYPE: "$CODE_DOWNLOAD_TYPE
-echo
-
-} # print_env_vars
-
-# Travis installations are running out of RAM
-# with large conda installations. Issue has been submitted here:
-# https://github.com/conda/conda/issues/1197
-# While we wait for a response, we'll try to clean up the conda
-# installation folder as much as possible
-conda_cleanup() {
-conda clean --index-cache
-conda clean --lock
-conda clean --tarballs -y
-conda clean --packages -y
-}
-
-
-# helper function to install cgat-core
-install_cgat_core() {
-
-log "install cgat core"
-
-OLDWD=`pwd`
-cd $CGAT_HOME
-
-if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
-   # get the latest version from Git Hub in zip format
-   curl -LOk https://github.com/cgat-developers/cgat-core/archive/$CORE_BRANCH.zip
-   unzip $CORE_BRANCH.zip
-   rm $CORE_BRANCH.zip
-   if [[ ${RELEASE} ]] ; then
-      NEW_NAME=`echo $CORE_BRANCH | sed 's/^v//g'`
-      mv cgat-core-$NEW_NAME/ cgat-core/
-   else
-      mv cgat-core-$CORE_BRANCH/ cgat-core/
-   fi
-elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
-   # get latest version from Git Hub with git clone
-   git clone --branch=$CORE_BRANCH https://github.com/cgat-developers/cgat-core.git
-elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
-   # get latest version from Git Hub with git clone
-   git clone --branch=$CORE_BRANCH git@github.com:cgat-developers/cgat-core.git
-else
-   report_error " Unknown download type for CGAT core... "
-fi
-
-cd cgat-core/
-
-# remove install_requires (no longer required with conda package)
-sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
-python setup.py develop
-
-if [[ $? -ne 0 ]] ; then
-   echo
-   echo " There was a problem doing: 'python setup.py develop' "
-   echo " Installation did not finish properly. "
-   echo
-   echo " Please submit this issue via Git Hub: "
-   echo " https://github.com/cgat-developers/cgat-apps/issues "
-   echo
-   print_env_vars
-
-fi # if-$?
-
-# revert setup.py if downloaded with git
-[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py
-
-# go back to old working directory
-cd $OLDWD
-
-} # install_cgat_core
-
-
-# proceed with conda installation
-conda_install() {
-
-log "installing conda"
-
-detect_cgat_installation
-
-if [[ -n "$UNINSTALL_DIR" ]] ; then
-
-   echo
-   echo " An installation of the CGAT code was found in: $UNINSTALL_DIR"
-   echo " Please use --location to install CGAT code in a different location "
-   echo " or uninstall the current version before proceeding."
-   echo
-   echo " Installation is aborted."
-   echo
-   exit 1
-
-fi
-
-# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_APPS
-get_cgat_env
-
-mkdir -p $CGAT_HOME
-cd $CGAT_HOME
-
-# select Miniconda bootstrap script depending on Operating System
-MINICONDA=
-
-if [[ `uname` == "Linux" ]] ; then
-
-   # Conda 4.4 breaks everything again!
-   # Conda 4.5 looks better
-   MINICONDA="Miniconda3-latest-Linux-x86_64.sh"
-   #MINICONDA="Miniconda3-4.3.31-Linux-x86_64.sh"
-
-elif [[ `uname` == "Darwin" ]] ; then
-
-   # Conda 4.4 breaks everything again!
-   # Conda 4.5 looks better
-   MINICONDA="Miniconda3-latest-MacOSX-x86_64.sh"
-   #MINICONDA="Miniconda3-4.3.31-MacOSX-x86_64.sh"
-
-else
-
-   echo
-   echo " Unsupported operating system detected. "
-   echo
-   echo " Aborting installation... "
-   echo
-   exit 1
-
-fi
-
-log "downloading miniconda"
-# download and install conda
-wget https://repo.continuum.io/miniconda/${MINICONDA} -O miniconda.sh;
-
-log "installing miniconda"
-bash miniconda.sh -b -p $CONDA_INSTALL_DIR
-source ${CONDA_INSTALL_DIR}/bin/activate
-hash -r
-
-# install cgat environment
-log "updating conda environment"
-# Conda 4.4 breaks everything again!
-# Conda 4.5 looks better
-#conda install --quiet --yes 'conda=4.3.33'
-conda update --all --yes
-conda info -a
-
-log "installing CGAT environment"
-# Now using conda environment files:
-# https://conda.io/docs/using/envs.html#use-environment-from-file
-
-[[ -z ${TRAVIS_BRANCH} ]] && TRAVIS_BRANCH=${INSTALL_BRANCH}
-
-curl -o env-apps.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-apps/${TRAVIS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_APPS}
-
-curl -o env-core.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-core/${CORE_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_CORE}
-
-conda env create --quiet --name ${CONDA_INSTALL_ENV} --file env-apps.yml
-conda env update --quiet --name ${CONDA_INSTALL_ENV} --file env-core.yml
-
-conda env export --name ${CONDA_INSTALL_ENV}
-
-# activate cgat environment
-source $CONDA_INSTALL_DIR/bin/activate $CONDA_INSTALL_ENV
-
-log "installing CGAT code into conda environment"
-# if installation is 'devel' (outside of travis), checkout latest version from github
-if [[ -z ${TRAVIS_INSTALL} ]] ; then
-
-   DEV_RESULT=0
-
-   # TO-DO: after code release, INSTALL_PRODUCTION will use pip rather than github
-   if [[ $INSTALL_PRODUCTION ]] || [[ $INSTALL_DEVEL ]] || [[ $JENKINS_INSTALL ]] ; then
-
-      # install extra deps
-      curl -o env-extra.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-apps/${TRAVIS_BRANCH}/conda/environments/apps-extra.yml
-      conda env update --quiet --file env-extra.yml
-      conda env export --name cgat-a
-
-      # download the code out of jenkins
-      if [[ -z ${JENKINS_INSTALL} ]] ; then
-
-         # make sure you are in the CGAT_HOME folder
-         cd $CGAT_HOME
-
-         if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
-            # get the latest version from Git Hub in zip format
-            curl -LOk https://github.com/cgat-developers/cgat-apps/archive/$INSTALL_BRANCH.zip
-            unzip $INSTALL_BRANCH.zip
-            rm $INSTALL_BRANCH.zip
-            if [[ ${RELEASE} ]] ; then
-               NEW_NAME=`echo $INSTALL_BRANCH | sed 's/^v//g'`
-               mv cgat-apps-$NEW_NAME/ cgat-apps/
-            else
-               mv cgat-apps-$INSTALL_BRANCH/ cgat-apps/
-            fi
-         elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
-            # get latest version from Git Hub with git clone
-            git clone --branch=$INSTALL_BRANCH https://github.com/cgat-developers/cgat-apps.git
-         elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
-            # get latest version from Git Hub with git clone
-            git clone --branch=$INSTALL_BRANCH git@github.com:cgat-developers/cgat-apps.git
-         else
-            report_error " Unknown download type for CGAT code... "
-         fi
-
-         # make sure you are in the CGAT_HOME/cgat-apps folder
-         cd $CGAT_HOME/cgat-apps
-
-      fi
-
-      # Set up other environment variables
-      setup_env_vars
-
-      # install cgat-core
-      install_cgat_core
-
-      # brute force: modify console_scripts variable/entry point for cgat command
-      sed -i'' -e 's/CGATScripts/scripts/g' setup.py
-
-      # Python preparation
-      # remove install_requires (no longer required with conda package)
-      sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-      sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
-      python setup.py develop
-
-      if [[ $? -ne 0 ]] ; then
-         echo
-         echo " There was a problem doing: 'python setup.py develop' "
-         echo " Installation did not finish properly. "
-         echo
-         echo " Please submit this issue via Git Hub: "
-         echo " https://github.com/cgat-developers/cgat-apps/issues "
-	 echo
-
-         print_env_vars
-
-      fi # if-$?
-
-      # revert setup.py if downloaded with git
-      [[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py
-
-      # environment pinning
-      # python scripts/conda.py
-
-   fi # if INSTALL_DEVEL
-
-   # check whether conda create went fine
-   if [[ $DEV_RESULT -ne 0 ]] ; then
-      echo
-      echo " There was a problem installing the code with conda. "
-      echo " Installation did not finish properly. "
-      echo
-      echo " Please submit this issue via Git Hub: "
-      echo " https://github.com/cgat-developers/cgat-apps/issues "
-      echo
-
-      print_env_vars
-
-   else
-      clear
-      echo
-      echo " The code was successfully installed!"
-      echo
-      echo " To activate the CGAT environment type: "
-      echo " $ source $CONDA_INSTALL_DIR/etc/profile.d/conda.sh"
-      echo " $ conda activate base"
-      echo " $ conda activate $CONDA_INSTALL_ENV"
-      [[ $INSTALL_PRODUCTION ]] && echo " cgat --help"
-      echo
-      echo " To deactivate the environment, use:"
-      echo " $ conda deactivate"
-      echo
-   fi # if-$ conda create
-
-fi # if travis install
-
-} # conda install
-
-
-# test code with conda install
-conda_test() {
-
-log "starting conda_test"
-
-# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_APPS
-get_cgat_env
-
-setup_env_vars
-
-# setup environment and run tests
-if [[ $TRAVIS_INSTALL ]] || [[ $JENKINS_INSTALL ]] ; then
-
-   # enable Conda env
-   log "activating CGAT conda environment"
-   source $CONDA_INSTALL_DIR/bin/activate $CONDA_INSTALL_ENV
-
-   # show conda environment used for testing
-   conda env export
-
-   # install cgat-core
-   install_cgat_core
-
-   # python preparation
-   log "install CGAT code into conda environment"
-   cd $CGAT_HOME
-   # remove install_requires (no longer required with conda package)
-   sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-   sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
-   python setup.py develop
-
-   log "starting tests"
-   # run nosetests
-   if [[ $TEST_ALL ]] ; then
-      log "test_import.py" && nosetests -v tests/test_import.py && \
-      log "test_style.py" && nosetests -v tests/test_style.py && \
-      echo -e "restrict:\n    manifest:\n" > tests/_test_commandline.yml && \
-      log "test_commandline" && nosetests -v tests/test_commandline.py && \
-      log "test_scripts" && nosetests -v tests/test_scripts.py ;
-   elif [[ $TEST_IMPORT ]] ; then
-      nosetests -v tests/test_import.py ;
-   elif [[ $TEST_STYLE ]] ; then
-      nosetests -v tests/test_style.py ;
-   elif [[ $TEST_CMDLINE ]] ; then
-      echo -e "restrict:\n    manifest:\n" > tests/_test_commandline.yml
-      nosetests -v tests/test_commandline.py ;
-   elif [[ $TEST_PRODUCTION_SCRIPTS  ]] ; then
-      echo -e "restrict:\n    manifest:\n" > tests/_test_scripts.yml
-      nosetests -v tests/test_scripts.py ;
-   else
-      nosetests -v tests/test_scripts.py ;
-   fi
-
-else
-
-   source $CONDA_INSTALL_DIR/bin/activate $CONDA_INSTALL_ENV
-   RET=$( (conda list | grep cgat-scripts) || true )
-
-   if [[ -z "${RET}" ]] ; then
-      # this is "cgat-devel" so tests can be run
-
-      # make sure you are in the CGAT_HOME/cgat-apps folder
-      cd $CGAT_HOME/cgat-apps
-
-      # remove install_requires (no longer required with conda package)
-      sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-      sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
-      python setup.py develop
-      OUTPUT_DIR=`pwd`
-
-      # run tests
-      /usr/bin/time -o test_import.time -v nosetests -v tests/test_import.py >& test_import.out
-      if [[ $? -eq 0 ]] ; then
-         echo
-         echo " test_import.py passed successfully! "
-         echo
-      else
-         echo
-         echo " test_import.py failed. Please see $OUTPUT_DIR/test_import.out file for detailed output. "
-         echo
-
-         print_env_vars
-
-      fi
-
-      /usr/bin/time -o test_scripts.time -v nosetests -v tests/test_scripts.py >& test_scripts.out
-      if [[ $? -eq 0 ]] ; then
-         echo
-         echo " test_scripts.py passed successfully! "
-         echo
-      else
-         echo
-         echo " test_scripts.py failed. Please see $OUTPUT_DIR/test_scripts.out file for detailed output. "
-         echo
-
-         print_env_vars
-
-      fi
-
-   else
-      # in this case, the installation found was "cgat-scripts" so no need to run tests
-      echo
-      echo " You installed the cgat-scripts, which has been properly tested before. "
-      echo " No need to test. Exiting now... "
-      echo
-
-      exit 0
-   fi
-
-fi # if travis or jenkins
-
-} # conda_test
-
-
-# update conda installation
-conda_update() {
-
-# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_APPS
-get_cgat_env
-
-source $CONDA_INSTALL_DIR/bin/activate $CONDA_INSTALL_ENV
-conda update --all
-
-if [[ ! $? -eq 0 ]] ; then
-
-   echo
-   echo " There was a problem updating the installation. "
-   echo
-   echo " Please submit this issue via Git Hub: "
-   echo " https://github.com/cgat-developers/cgat-apps/issues "
-   echo
-
-else
-
-   echo
-   echo " All packages were succesfully updated. "
-   echo
-
-fi
-
-} # conda_update
-
-
-# unistall CGAT code collection
-uninstall() {
-
-detect_cgat_installation
-
-if [[ -z "$UNINSTALL_DIR" ]] ; then
-
-   echo
-   echo " The location of the CGAT code was not found. "
-   echo " Please uninstall manually."
-   echo
-   exit 1
-
-else
-
-   rm -rf $UNINSTALL_DIR
-   if [[ $? -eq 0 ]] ; then
-      echo
-      echo " CGAT code successfully uninstalled."
-      echo
-      exit 0
-   else
-      echo
-      echo " There was a problem uninstalling the CGAT code."
-      echo " Please uninstall manually."
-      echo
-      exit 1
-   fi
-fi
-
-}
-
-
-# test whether --git and --git-ssh download is doable
-test_git() {
-   git --version >& /dev/null || GIT_AVAIL=$?
-   if [[ $GIT_AVAIL -ne 0 ]] ; then
-      echo
-      echo " Git is not available but --git or --git-ssh option was given."
-      echo " Please rerun this script on a computer with git installed "
-      echo " or try again without --git or --git-ssh"
-      report_error " "
-   fi
-}
-
-
-# test whether --git-ssh download is doable
-test_git_ssh() {
-   ssh-add -L >& /dev/null || SSH_KEYS_LOADED=$?
-   if [[ $SSH_KEYS_LOADED -ne 0 ]] ; then
-      echo
-      echo " Please load your ssh keys for GitHub before proceeding!"
-      echo
-      echo " Try: "
-      echo " 1. eval \$(ssh-agent)"
-      echo " 2. ssh-add ~/.ssh/id_rsa # or the file where your private key is"
-      report_error " and run this script again. "
-   fi
-}
-
-
-# don't mix branch and release options together
-test_mix_branch_release() {
-   # don't mix branch and release options together
-   if [[ $RELEASE ]] ; then
-      if [[ "$INSTALL_BRANCH" != "master" ]] ; then
-         echo
-         echo " You cannot mix git branches and releases for the installation."
-         echo
-         echo " Your input was: "$SCRIPT_PARAMS
-         report_error " Please either use branches or releases but not both."
-      fi
-   fi
-}
-
-
-# test whether a branch exists in the cgat-core repository
-# https://stackoverflow.com/questions/12199059/how-to-check-if-an-url-exists-with-the-shell-and-probably-curl
-test_core_branch() {
-   RELEASE_TEST=0
-   curl --output /dev/null --silent --head --fail https://raw.githubusercontent.com/cgat-developers/cgat-core/${CORE_BRANCH}/README.md || RELEASE_TEST=$?
-   if [[ ${RELEASE_TEST} -ne 0 ]] ; then
-      echo
-      echo " The branch provided for cgat-core does not exist: ${CORE_BRANCH}"
-      echo
-      echo " Please have a look at valid branches here: "
-      echo " https://github.com/cgat-developers/cgat-core/branches"
-      echo
-      report_error " Please use a valid branch and try again."
-   fi
-}
-
-
-# test whether a release exists or not
-# https://stackoverflow.com/questions/12199059/how-to-check-if-an-url-exists-with-the-shell-and-probably-curl
-test_release() {
-   RELEASE_TEST=0
-   curl --output /dev/null --silent --head --fail https://raw.githubusercontent.com/cgat-developers/cgat-apps/${RELEASE}/README.rst || RELEASE_TEST=$?
-   if [[ ${RELEASE_TEST} -ne 0 ]] ; then
-      echo
-      echo " The release number provided does not exist: ${RELEASE}"
-      echo
-      echo " Please have a look at valid releases here: "
-      echo " https://github.com/cgat-developers/cgat-apps/releases"
-      echo
-      echo " An example of valid release is: --release v0.4.0"
-      report_error " Please use a valid release and try again."
-   fi
-}
-
-
-# test whether a C/C++ compiler is available
-test_compilers() {
-   which gcc &> /dev/null || report_error " C compiler not found "
-   which g++ &> /dev/null || report_error " C++ compiler not found "
-}
-
-
-# clean up environment
-# deliberately use brute force
-cleanup_env() {
-   set +e
-   source deactivate >& /dev/null || true
-   source deactivate >& /dev/null || true
-   unset -f conda || true
-   unset PYTHONPATH || true
-   # Next actions disabled. Please see:
-   # https://github.com/cgat-developers/cgat-core/issues/44
-   #module purge >& /dev/null || true
-   #mymodule purge >& /dev/null || true
-   set -e
-}
-
-
-# function to display help message
-help_message() {
-echo
-echo " This script uses Conda to install cgat-apps. To proceed, please type:"
-echo " ./install.sh --devel [--location </full/path/to/folder/without/trailing/slash>]"
-echo
-echo " The default install folder will be: $HOME/cgat-install"
-echo
-echo " It will create a new Conda environment ready to run the CGAT code."
-echo
-echo " It is also possible to install/test a specific branch of the code on github:"
-echo " ./install.sh --devel --branch <name-of-branch> [--location </full/path/to/folder/without/trailing/slash>]"
-echo
-echo " By default, cgat-apps will install the master branch of cgat-core:"
-echo " https://github.com/cgat-developers/cgat-core"
-echo
-echo " Change that with:"
-echo " ./install.sh --devel --core-branch <name-of-branch>"
-echo
-echo " To test the installation:"
-echo " ./install.sh --test [--location </full/path/to/folder/without/trailing/slash>]"
-echo
-echo " To update the Conda packages:"
-echo " ./install.sh --update [--location </full/path/to/folder/without/trailing/slash>]"
-echo
-echo " To uninstall the CGAT code:"
-echo " ./install.sh --uninstall [--location </full/path/to/folder/without/trailing/slash>]"
-echo
-echo " Please submit any issues via Git Hub:"
-echo " https://github.com/cgat-developers/cgat-apps/issues"
-echo
-exit 1
-} # help_message
-
-# the script starts here
-
-cleanup_env
-test_compilers
-
-if [[ $# -eq 0 ]] ; then
-
-   help_message
-
-fi
-
-# travis execution
-TRAVIS_INSTALL=
-# jenkins testing
-JENKINS_INSTALL=
-# conda installation type
-INSTALL_PRODUCTION=
-INSTALL_DEVEL=
-# test current installation
-INSTALL_TEST=
-# update current installation
-INSTALL_UPDATE=
-# uninstall CGAT code
-UNINSTALL=
-UNINSTALL_DIR=
-# where to install CGAT code
-CGAT_HOME=
-# how to download CGAT code:
-# 0 = as zip (default)
-# 1 = git clone with https
-# 2 = git clone with ssh
-CODE_DOWNLOAD_TYPE=0
-# which github branch to use (default: master)
-INSTALL_BRANCH="master"
-# which github branch to use for cgat-core (default: master)
-CORE_BRANCH="master"
-# rename conda environment
-CONDA_INSTALL_ENV=
-# type of installation
-CONDA_INSTALL_TYPE_APPS=
-CONDA_INSTALL_TYPE_CORE=
-# Install a released version?
-RELEASE=
-
-# parse input parameters
-# https://stackoverflow.com/questions/402377/using-getopts-in-bash-shell-script-to-get-long-and-short-command-line-options
-# https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
-
-while [[ $# -gt 0 ]]
-do
-key="$1"
-
-case $key in
-
-    --help)
-    help_message
-    ;;
-
-    --travis)
-    TRAVIS_INSTALL=1
-    shift # past argument
-    ;;
-
-    --jenkins)
-    JENKINS_INSTALL=1
-    shift # past argument
-    ;;
-
-    --zip)
-    CODE_DOWNLOAD_TYPE=0
-    shift
-    ;;
-
-    --git)
-    CODE_DOWNLOAD_TYPE=1
-    shift
-    test_git
-    ;;
-
-    --git-ssh)
-    CODE_DOWNLOAD_TYPE=2
-    shift
-    test_git
-    test_git_ssh
-    ;;
-
-    --production)
-    INSTALL_PRODUCTION=1
-    shift
-    ;;
-
-    --devel)
-    INSTALL_DEVEL=1
-    shift
-    ;;
-
-    --test)
-    INSTALL_TEST=1
-    shift
-    ;;
-
-    --update)
-    INSTALL_UPDATE=1
-    shift
-    ;;
-
-    --uninstall)
-    UNINSTALL=1
-    shift
-    ;;
-
-    --location)
-    CGAT_HOME="$2"
-    shift 2
-    ;;
-
-    --branch)
-    INSTALL_BRANCH="$2"
-    test_mix_branch_release
-    shift 2
-    ;;
-
-    --core-branch)
-    CORE_BRANCH="$2"
-    test_core_branch
-    shift 2
-    ;;
-
-    --release)
-    RELEASE="$2"
-    test_mix_branch_release
-    test_release
-    INSTALL_BRANCH="$2"
-    shift 2
-    ;;
-
-    --env-name)
-    CONDA_INSTALL_ENV="$2"
-    shift 2
-    ;;
-
-    *)
-    echo
-    echo
-    echo " Wrong input: ${SCRIPT_NAME} ${SCRIPT_PARAMS}"
-    echo
-    help_message
-    ;;
-
-esac
-done
-
-# sanity check 1: don't mix production and development installs
-if [[ $INSTALL_PRODUCTION ]] && [[ $INSTALL_DEVEL ]] ; then
-
-   report_error " Incorrect input arguments: mixing --production and --devel is not permitted. "
-
-fi
-
-# sanity check 2: make sure one installation option is selected
-if [[ -z $INSTALL_TEST ]] && \
-   [[ -z $INSTALL_PRODUCTION ]] && \
-   [[ -z $INSTALL_DEVEL ]] && \
-   [[ -z $TRAVIS_INSTALL ]] && \
-   [[ -z $JENKINS_INSTALL ]] ; then
-
-   report_error " You need to select either --devel or --production. "
-
-fi
-
-# sanity check 3: make sure there is space available in the destination folder (10 GB) in 512-byte blocks
-[[ -z ${TRAVIS_INSTALL} ]] && \
-mkdir -p ${CGAT_HOME} && \
-[[ `df -P ${CGAT_HOME} | awk '/\// {print $4}'` -lt 20971520 ]] && \
-   report_error " Not enough disk space available on the installation folder: "$CGAT_HOME
-
-# perform actions according to the input parameters processed
-if [[ $TRAVIS_INSTALL ]] || [[ $JENKINS_INSTALL  ]] ; then
-
-  conda_install
-  conda_test
-
-else
-
-  if [[ $INSTALL_PRODUCTION ]] || [[ $INSTALL_DEVEL ]] ; then
-     conda_install
-  fi
-
-  if [[ $INSTALL_TEST ]] ; then
-     conda_test
-  fi
-
-  if [[ $INSTALL_UPDATE ]] ; then
-     conda_update
-  fi
-
-  if [[ $UNINSTALL ]] ; then
-     uninstall
-  fi
-
-fi # if-variables
diff --git a/requires.txt b/requires.txt
deleted file mode 100644
index e69de29bb..000000000
diff --git a/setup.py b/setup.py
index adb4ccd73..cd7a2ef0d 100644
--- a/setup.py
+++ b/setup.py
@@ -137,37 +137,6 @@ def is_exe(fpath):
 HTTPS_REQUIREMENT = re.compile(
     r'^-e (?P<link>.*).+#(?P<package>.+)-(?P<version>\d(?:\.\d)*)$')
 install_requires = []
-dependency_links = []
-
-for requirement in (
-        l.strip() for l in open('requires.txt') if not l.startswith("#")):
-    match = REPO_REQUIREMENT.match(requirement)
-    if match:
-        assert which(match.group('vcs')) is not None, \
-            ("VCS '%(vcs)s' must be installed in order to "
-             "install %(link)s" % match.groupdict())
-        install_requires.append("%(package)s==%(version)s" % match.groupdict())
-        dependency_links.append(match.group('link'))
-        continue
-
-    if requirement.startswith("https"):
-        install_requires.append(requirement)
-        continue
-
-    match = HTTPS_REQUIREMENT.match(requirement)
-    if match:
-        install_requires.append("%(package)s>=%(version)s" % match.groupdict())
-        dependency_links.append(match.group('link'))
-        continue
-
-    install_requires.append(requirement)
-
-if major == 2:
-    install_requires.extend(['web.py>=0.37',
-                             'xlwt>=0.7.4',
-                             'matplotlib-venn>=0.5'])
-elif major == 3:
-    pass
 
 cgat_packages = find_packages()
 cgat_package_dirs = {'cgat': 'cgat'}
@@ -317,7 +286,6 @@ def is_exe(fpath):
     },
     # dependencies
     install_requires=install_requires,
-    dependency_links=dependency_links,
     # extension modules
     ext_modules=extensions,
     cmdclass={'build_ext': build_ext},
diff --git a/tests/test_commandline.py b/tests/test_commandline.py
index 68e8d124f..0feb1d953 100644
--- a/tests/test_commandline.py
+++ b/tests/test_commandline.py
@@ -1,5 +1,6 @@
-'''test_commandline - test coding style confirmation of CGAT code
-===========================================================
+'''
+test_commandline - Tests coding style conformity of CGAT code collection.
+==========================================================================
 
 :Author: Andreas Heger
 :Release: $Id$
@@ -8,24 +9,18 @@
 
 Purpose
 -------
-
-This script test the command line usage of all scripts in the
-CGAT code collection.
-
-This script is best run within nosetests::
+This script tests the command line usage of all scripts in the CGAT code collection.
+It's recommended to run this within nosetests for efficiency and coverage:
 
    nosetests tests/test_commandline.py --nocapture
 
+Before running these tests, ensure to execute:
 
-.. note::
-
-   Make sure to run::
-
-       python setup.py develop
-
-   Before running these tests.
+   python setup.py develop
 
+to make all package scripts available for import and testing.
 '''
+
 import glob
 import os
 import importlib
@@ -33,217 +28,160 @@
 import re
 import sys
 import copy
-import platform
+import argparse
 
 from nose.tools import ok_
 import cgatcore.experiment as E
 import cgatcore.iotools as iotools
 import TestUtils
 
-# handle to original E.Start function
-ORIGINAL_START = None
+# Preserve the original E.Start function for later restoration
+ORIGINAL_START = E.start
 
-# Parser object collected from child script
+# Placeholders for parser object and tested script's module
 PARSER = None
+TESTED_MODULE = None
 
-# DIRECTORIES to examine for python modules/scripts
+# Directories to examine for Python modules/scripts
 EXPRESSIONS = (
-    ('tools', 'cgat/tools/*.py'),)
+    ('tools', 'cgat/tools/*.py'),
+)
 
+# Files to exclude from checks
 EXCLUDE = [
     "__init__.py",
     "version.py",
     "cgat.py",
-    "gtf2table.py",  # fails with pysam include issue
-    "bed2table.py",  # fails with pysam include issue
-    "fasta2bed.py",   # fails because of pybedtools rebuild
+    "gtf2table.py",   # Fails with pysam include issue
+    "bed2table.py",   # Fails with pysam include issue
+    "fasta2bed.py",   # Fails due to pybedtools rebuild requirements
 ]
 
-# Filename with the black/white list of options.
-# The file is a tab-separated with the first column
-# an option name and the second field a marker.
-# Possible markers are:
-# ok = whitelist - this option is ok.
-# 'bad', 'rename', '?', '' - this option is not ok.
+# Filename for the black/white list of options
 FILENAME_OPTIONLIST = "tests/option_list.tsv"
 
 
 class DummyError(Exception):
+    """Custom exception for controlling test flow."""
     pass
 
 
 def filter_files(files):
-    '''filter list of files according to filters set in
-    configuration file tests/_test_commandline.yml'''
-
-    # directory location of tests
+    '''Filter list of files according to filters set in the configuration file tests/_test_commandline.yml'''
     testing_dir = TestUtils.get_tests_directory()
-
-    # the config file
     config_file = os.path.join(testing_dir, "_test_commandline.yml")
 
     if os.path.exists(config_file):
-        config = yaml.safe_load(open(config_file))
-        if config is not None:
-            if "restrict" in config and config["restrict"]:
+        with open(config_file) as cf:
+            config = yaml.safe_load(cf)
+            if config and "restrict" in config:
                 values = config["restrict"]
                 if "manifest" in values:
-                    # take scripts defined in the MANIFEST.in file
-                    scriptdirs = [x for x in open("MANIFEST.in")
-                                  if x.startswith("include CGAT/tools") and
-                                  x.endswith(".py\n")]
-
-                    take = set([re.sub("include\s*", "",
-                                       x[:-1]) for x in scriptdirs])
+                    scriptdirs = [x.strip() for x in open("MANIFEST.in")
+                                  if x.startswith("include CGAT/tools") and x.endswith(".py\n")]
+                    take = set(re.sub("include\s*", "", x) for x in scriptdirs)
                     files = [x for x in files if x in take]
-
                 if "regex" in values:
                     rx = re.compile(values["regex"])
-                    files = filter(rx.search, files)
+                    files = list(filter(rx.search, files))
     return files
 
 
 def LocalStart(parser, *args, **kwargs):
-    '''stub for E.start - set return_parser argument to true'''
+    '''Stub for E.start - captures the parser for inspection.'''
     global PARSER
-    d = copy.copy(kwargs)
-    d.update({'return_parser': True})
-    PARSER = ORIGINAL_START(parser, **d)
+    kwargs.update({'return_parser': True})
+    PARSER = ORIGINAL_START(parser, **kwargs)
     raise DummyError()
 
 
 def load_script(script_name):
+    '''Attempts to import a script as a module for inspection.'''
+    script_path = os.path.splitext(script_name)[0]
+    script_dir, script_base = os.path.split(script_path)
+    module_name = ".".join(filter(None, [script_dir.replace(os.sep, '.'), script_base]))
 
-    # call other script
-    prefix, suffix = os.path.splitext(script_name)
-
-    dirname = os.path.relpath(os.path.dirname(script_name))
-    basename = os.path.basename(script_name)[:-3]
+    # Remove compiled files to ensure fresh import
+    compiled_script = script_path + ".pyc"
+    if os.path.exists(compiled_script):
+        os.remove(compiled_script)
 
-    if os.path.exists(prefix + ".pyc"):
-        try:
-            os.remove(prefix + ".pyc")
-        except OSError:
-            pass
-
-    modulename = ".".join((re.sub("/", ".", dirname), basename))
     try:
-        module = importlib.import_module(modulename)
-    except ImportError as msg:
-        sys.stderr.write('could not import %s - skipped: %s\n' %
-                         (modulename, msg))
-        module = None
-
-    return module, modulename
+        module = importlib.import_module(module_name)
+    except ImportError as e:
+        sys.stderr.write(f'ImportError for {module_name}: {e}\n')
+        return None, None
 
-
-def check_option(option, script_name, map_option2action):
-    '''import script and get command line options.
-
-    Test command line options for conformity.
-    '''
-    if option in map_option2action:
-        ok_(option in map_option2action,
-            'option %s:%s unknown')
-        ok_(map_option2action[option] == "ok",
-            'option %s:%s wrong: action="%s"' %
-            (script_name, option, map_option2action[option]))
-
-
-def fail_(msg):
-    '''create test that fails with *msg*.'''
-    ok_(False, msg)
+    return module, module_name
 
 
 def test_cmdline():
-    '''test style of scripts
-    '''
-
-    # start script in order to build the command line parser
+    '''Test command line interfaces of scripts for style and conformity.'''
     global ORIGINAL_START
-    if ORIGINAL_START is None:
-        ORIGINAL_START = E.start
-    # read the first two columns
-    map_option2action = iotools.read_map(
+
+    # Load option actions from list
+    option_actions = iotools.read_map(
         iotools.open_file(FILENAME_OPTIONLIST),
         columns=(0, 1),
-        has_header=True)
-
-    files = []
-    for label, expression in EXPRESSIONS:
-        f = glob.glob(expression)
-        files.extend(sorted(f))
+        has_header=True
+    )
 
+    # Compile list of scripts to test
+    files = [f for label, expr in EXPRESSIONS for f in glob.glob(expr)]
     files = filter_files(files)
 
-    # make sure to use the current working directory as
-    # primary lookup.
+    # Prioritise the current directory for module lookup
     sys.path.insert(0, ".")
 
-    # files = [
-    #    'scripts/check_db.py',
-    #    'scripts/cgat_build_report_page.py']
-
-    for f in files:
-        if os.path.isdir(f):
-            continue
-        if os.path.basename(f) in EXCLUDE:
+    for script in files:
+        if os.path.isdir(script) or os.path.basename(script) in EXCLUDE:
             continue
 
-        script_name = os.path.abspath(f)
-        pyxfile = (os.path.join(os.path.dirname(f), "_") +
-                   os.path.basename(f) + "x")
-
-        fail_.description = script_name
-        # check if script contains getopt
-        with iotools.open_file(script_name) as inf:
-            if "getopt" in inf.read():
-                yield (fail_,
-                       "script uses getopt directly: %s" % script_name)
-                continue
-
-        module, modulename = load_script(script_name)
-        if module is None:
-            yield (fail_,
-                   "module could not be imported: %s\n" % script_name)
+        script_name = os.path.abspath(script)
+        module, module_name = load_script(script)
+        if not module:
+            yield fail_, f"Module {script_name} could not be imported."
             continue
+
+        # Replace the start function to capture parser
         E.start = LocalStart
 
+        # Attempt to run script's main function to access its parser
         try:
-            module.main(argv=["dummy", "--help"])
-        except AttributeError:
-            yield (fail_,
-                   "no main method in %s\n" % script_name)
-            ok_(False, "no main method in %s" % script_name)
-        except SystemExit:
-            yield (fail_,
-                   "script does not use E.start() %s\n" % script_name)
+            module.main(argv=["--help"])
         except DummyError:
+            # Expected flow interruption by LocalStart
             pass
+        except Exception as e:
+            yield fail_, f"Error invoking main of {script_name}: {e}"
+            continue
+
+        if PARSER:
+            for action in PARSER._actions:  # Iterate through the actions stored in the parser
+                if isinstance(action, argparse._HelpAction):  # Skip help actions
+                    continue
+                opt_strings = action.option_strings  # Get the list of CLI flags
+                if not opt_strings:  # This skips positional arguments
+                    continue
+                for opt_string in opt_strings:
+                    if opt_string.startswith("--"):
+                        opt_string = opt_string[2:]
+                    yield check_option, opt_string, script_name, option_actions
 
-        for option in PARSER.parse_args(parser):
-            print("=================")
-            print(option)
-            # ignore options added by optparse
-            if option.dest is None:
-                continue
+        # Reset module to avoid conflicts
+        if module_name in sys.modules:
+            del sys.modules[module_name]
 
-            optstring = option.get_opt_string()
-            if optstring.startswith("--"):
-                optstring = optstring[2:]
 
-            check_option.description = script_name + ":" + optstring
+def check_option(option, script_name, option_actions):
+    print(f"Checking option: {option} in script: {script_name}")  # Diagnostic print
+    assert option in option_actions, f"Option {option} in script {script_name} is unknown or not allowed."
+    assert option_actions[option] == "ok", f"Option {option} in script {script_name} is not allowed."
 
-            yield(check_option, optstring, os.path.abspath(f),
-                  map_option2action)
 
-        # clear up
-        del sys.modules[modulename]
+def fail_(msg):
+    '''Generate a failing test with the provided message.'''
+    ok_(False, msg)
 
-        # scripts with pyximport need special handling.
-        #
-        # Multiple imports of pyximport seems to create
-        # some confusion - here, clear up sys.meta_path after
-        # each script
-        if os.path.exists(pyxfile):
-            sys.meta_path = []
+# Reset E.start to its original function after testing
+E.start = ORIGINAL_START