diff --git a/.bumpversion.cfg b/.bumpversion.cfg
new file mode 100644
index 0000000..86430d7
--- /dev/null
+++ b/.bumpversion.cfg
@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 0.1.0
+commit = True
+tag = True
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:dna_mutator/version.py]
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..7a21eb1
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,25 @@
+name: build
+
+on: [push, workflow_dispatch]
+
+jobs:
+ build:
+
+ runs-on: ubuntu-22.04
+
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.9
+ uses: actions/setup-python@v2
+ with:
+ python-version: '3.9'
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install pytest pytest-cov
+ - name: Test pip installation
+ run: |
+ pip install -e .
+ - name: Test with pytest
+ run: |
+ python -m pytest --cov dna_mutator
diff --git a/.gitignore b/.gitignore
index 82f9275..b6e4761 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,6 +20,7 @@ parts/
sdist/
var/
wheels/
+pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
@@ -49,7 +50,6 @@ coverage.xml
*.py,cover
.hypothesis/
.pytest_cache/
-cover/
# Translations
*.mo
@@ -72,7 +72,6 @@ instance/
docs/_build/
# PyBuilder
-.pybuilder/
target/
# Jupyter Notebook
@@ -83,9 +82,7 @@ profile_default/
ipython_config.py
# pyenv
-# For a library or package, you might want to ignore these files since the code is
-# intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -94,24 +91,7 @@ ipython_config.py
# install all needed dependencies.
#Pipfile.lock
-# poetry
-# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-# This is especially recommended for binary packages to ensure reproducibility, and is more
-# commonly ignored for libraries.
-# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-# in version control.
-# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/
# Celery stuff
@@ -147,16 +127,3 @@ dmypy.json
# Pyre type checker
.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-# and can be added to the global gitignore or merged into this file. For a more nuclear
-# option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..beb22c6
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Edinburgh Genome Foundry
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
index 058d576..9b561c2 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,41 @@
-# Mutator
\ No newline at end of file
+
+
+
+
+# DNA Mutator
+
+
+[](https://github.com/Edinburgh-Genome-Foundry/dna_mutator/actions/workflows/build.yml)
+
+Create variants of DNA sequences.
+
+This repository is based on the software code of a dissertation project (B237870) for the MSc Bioinformatics program at the University of Edinburgh.
+
+## Install
+
+```bash
+pip install git+https://github.com/Edinburgh-Genome-Foundry/mutator.git
+```
+
+## Usage
+
+```python
+import dna_mutator as mutator
+record = mutator.Mutator.read_genbank("EGF.gb")
+mut = mutator.Mutator(record)
+mut.DelN()
+mut.write_all_records("variants")
+```
+
+## Versioning
+
+DNA Mutator uses the [semantic versioning](https://semver.org) scheme.
+
+## License = MIT
+
+DNA Mutator is free/libre and open-source software, which means the users have the freedom to run, study, change and distribute the software.
+
+DNA Mutator was written at the [Edinburgh Genome Foundry](https://edinburgh-genome-foundry.github.io/)
+by [B237870](https://github.com/B237870-2024) and [Peter Vegh](https://github.com/veghp).
+
+Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh
diff --git a/dna_mutator/Mutator.py b/dna_mutator/Mutator.py
new file mode 100644
index 0000000..479656f
--- /dev/null
+++ b/dna_mutator/Mutator.py
@@ -0,0 +1,148 @@
+import os
+import random
+
+import pandas
+
+from Bio import SeqIO
+from Bio.Seq import Seq, MutableSeq
+from Bio.SeqRecord import SeqRecord
+from Bio.SeqFeature import SeqFeature, FeatureLocation
+
+
+class Mutator:
+ """Class to generate simulations of structural and single nucleotide variants.
+
+
+ **Parameters**
+
+ **reference**
+ > A `SeqRecord` instance.
+
+ **library_size**
+ > Library size (`int`).
+ """
+
+ def __init__(self, reference, library_size=10):
+ self.reference = reference
+ self.library_size = library_size
+ self.variant_records = []
+
+ def write_sample_sheet(self, csv_file):
+ """Create a sample sheet (for use with Sequeduct)"""
+ barcode_dir = [
+ "barcode" + ("{0:02d}".format(i + 1))
+ for i in range(len(self.variant_records))
+ ]
+
+ variants = [variant_record.id for variant_record in self.variant_records]
+ df_variants = pandas.DataFrame({"Sample": variants, "Barcode_dir": barcode_dir})
+ df_variants.to_csv(csv_file, index=False)
+
+ @staticmethod
+ def subtract_bases(seq, pos, n):
+ """Substract N bases from a sequence
+
+
+ **Parameters**
+
+ **seq**
+ > `Seq` instance.
+
+ **pos**
+ > Location of change (`int`).
+
+ **n**
+ > Number of bases to subtract (`int`).
+ """
+ modified_sequence = MutableSeq(seq)
+ deleted_sequence = modified_sequence[pos : pos + n]
+ del modified_sequence[pos : pos + n]
+
+ return (
+ modified_sequence,
+ pos,
+ deleted_sequence,
+ )
+
+ @staticmethod
+ def get_random_pos(record, n=1):
+ """Get n different random positions in a record"""
+ positions = random.sample(range(0, len(record)), n)
+
+ return positions
+
+ @staticmethod
+ def read_genbank(genbank, use_file_name_as_id=True):
+ """Get the reference sequence and features from input file
+
+ **Parameters**
+
+ **genbank**
+ > Path to Genbank file (`str`).
+
+ **use_file_name_as_id**
+ > Replace record id and name with the filename (`bool`).
+ """
+ record = SeqIO.read(genbank, "genbank")
+ if use_file_name_as_id:
+ record.name = os.path.splitext(os.path.basename(genbank))[0]
+ record.id = record.name
+
+ return record
+
+ @staticmethod
+ def write_genbank(record, file_name):
+ """Write SeqRecord to a Genbank file"""
+ SeqIO.write(record, file_name, "gb")
+
+ def write_all_records(self, dir_name):
+ """Write original record and all variants into a directory"""
+ extension = ".gb" # standard file ext for GenBank files
+ os.mkdir(dir_name)
+ # ORIGINAL REFERENCE RECORD
+ ref_path = os.path.join(dir_name, self.reference.id + extension)
+ self.write_genbank(self.reference, ref_path)
+ # VARIANTS
+ for variant in self.variant_records:
+ variant_path = os.path.join(dir_name, variant.id)
+ self.write_genbank(variant, variant_path + extension)
+
+ def DelN(self, bases=1):
+ """Simulate N base deletion"""
+ positions = self.get_random_pos(self.reference, n=self.library_size)
+ for i in range(self.library_size):
+ position = positions[i]
+ modified_sequence, position, deleted_sequence = self.subtract_bases(
+ self.reference.seq, position, bases
+ )
+ if len(deleted_sequence) == 1: # show the letter if there's only one
+ suffix = str(deleted_sequence)
+ else:
+ suffix = str(len(deleted_sequence))
+ # We append the original name according to nomenclature:
+ variant_name = self.reference.id + "_" + str(position) + "D" + suffix
+ variant_record = SeqRecord(
+ Seq(modified_sequence),
+ id=variant_name,
+ name=variant_name,
+ annotations={"molecule_type": "DNA", "topology": "circular"},
+ )
+ label = "@mutator(del)"
+ description = (
+ "Deletion in position "
+ + str(position)
+ + " of "
+ + str(bases)
+ + " bases ("
+ + str(deleted_sequence)
+ + ")"
+ )
+ feature = SeqFeature(
+ FeatureLocation(position, position),
+ type="misc_feature",
+ id="@mutator",
+ qualifiers={"label": label, "note": description},
+ )
+ variant_record.features.append(feature)
+
+ self.variant_records.append(variant_record)
diff --git a/dna_mutator/__init__.py b/dna_mutator/__init__.py
new file mode 100644
index 0000000..e2aa00b
--- /dev/null
+++ b/dna_mutator/__init__.py
@@ -0,0 +1 @@
+from .Mutator import Mutator
diff --git a/dna_mutator/version.py b/dna_mutator/version.py
new file mode 100644
index 0000000..3dc1f76
--- /dev/null
+++ b/dna_mutator/version.py
@@ -0,0 +1 @@
+__version__ = "0.1.0"
diff --git a/images/egf.png b/images/egf.png
new file mode 100644
index 0000000..6e0f67e
Binary files /dev/null and b/images/egf.png differ
diff --git a/pypi-readme.rst b/pypi-readme.rst
new file mode 100644
index 0000000..db4e3d9
--- /dev/null
+++ b/pypi-readme.rst
@@ -0,0 +1,33 @@
+DNA Mutator
+=============================
+
+Creating variants of DNA sequences
+
+
+**Install:**
+
+.. code:: bash
+
+ pip install dna_mutator
+
+
+**Web documentation:**
+
+``_
+
+
+**Github page:**
+
+``_
+
+
+**License:** MIT, Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh
+
+
+More biology software
+---------------------
+
+.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
+ :target: https://edinburgh-genome-foundry.github.io/
+
+DNA Mutator is part of the `EGF Codons `_ synthetic biology software suite for DNA design, manufacturing and validation.
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..425474a
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,20 @@
+from setuptools import setup, find_packages
+
+version = {}
+with open("dna_mutator/version.py") as fp:
+ exec(fp.read(), version)
+
+setup(
+ name="dna_mutator",
+ version=version["__version__"],
+ author="B237870",
+ author_email="egf-software@ed.ac.uk",
+ description="Create variants of DNA sequences",
+ long_description=open("pypi-readme.rst").read(),
+ long_description_content_type="text/x-rst",
+ license="MIT",
+ keywords="biology dna",
+ packages=find_packages(exclude="docs"),
+ include_package_data=True,
+ install_requires=["biopython"],
+)
diff --git a/tests/test_Mutator.py b/tests/test_Mutator.py
new file mode 100644
index 0000000..91579e4
--- /dev/null
+++ b/tests/test_Mutator.py
@@ -0,0 +1,7 @@
+import pytest
+
+import dna_mutator
+
+
+def test_Mutator():
+ pass