Merge pull request #33 from samhorsfield96/docs

Updates docs and prevents warning message with biopython

.readthedocs.yaml

@@ -12,6 +12,12 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Optionally set the version of Python and requirements required to build your docs
 python:
    version: 3.8

README.md

@@ -14,9 +14,21 @@ ggCaller is available on Linux. If you are running Windows 10/11, Linux can be i
 
 We plan to get a MacOS version up and running in the future.
 
-NOTE: We are aware of issues installing from conda at the moment. We recommend installing via docker at this time.
+### Installation via conda/mamba
 
-### Installing with Docker (recommended)
+Install through [bioconda](http://bioconda.github.io/):
+
+```conda install ggcaller```
+
+If conda is not installed, first install [miniconda](https://docs.conda.io/en/latest/miniconda.html), then add the correct channels:
+
+```
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+```
+
+### Installing with Docker
 
 First, install [Docker](https://docs.docker.com/get-docker/) for your OS. If running with WSL2, you should still download Docker Desktop for Windows.
 
@@ -26,7 +38,7 @@ Then pull the latest image::
 
 To run ggCaller, run::
 
-	cd test && docker run --rm -it -v $(pwd):/workdir samhorsfield96/ggcaller:latest ggcaller --refs pneumo_CL_group2.txt
+	cd test && docker run --rm -it -v $(pwd):/workdir -v $(pwd):/data samhorsfield96/ggcaller:latest ggcaller --balrog-db /app/ggc_db --refs /workdir/pneumo_CL_group2_docker.txt --out /workdir/ggc_out
 
 ### Installation from source
 Required packages and versions can be found in ```environment_linux.yml``` and ```environment_macOS.yml``` depending on your operating system. In addition, a C++17 compiler (e.g. gcc >=7.3) is required.
@@ -46,20 +58,6 @@ cd ggCaller
 python setup.py install
 ```
 
-### Installation via conda
-
-Install through [bioconda](http://bioconda.github.io/):
-
-```conda install ggcaller```
-
-If conda is not installed, first install [miniconda](https://docs.conda.io/en/latest/miniconda.html), then add the correct channels:
-
-```
-conda config --add channels defaults
-conda config --add channels bioconda
-conda config --add channels conda-forge
-```
-
 ## Citation
 
 Please cite the ggCaller pre-print:

docs/advanced.rst

@@ -8,6 +8,7 @@ Input/output
 
 - ``--kmer``: value of k used to build Bifrost DBG (Default and max value = 31).
 - ``--all-seq-in-graph``: Output gene graph GML file with all DNA and amino acid sequences. Off by default due to large file size.
+- ``--balrog-db``: Path to an existing download of the balrog annotation database. If this does not exist, downloaded and placed in path for future use.
 
 Traversal and gene-calling cut-off settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/installation.rst

@@ -10,18 +10,18 @@ We plan to get a MacOS version up and running in the future.
     (which on many default Linux installations is
     run using ``python3`` rather than ``python``).
 
-Installing with Docker (recommended)
+Installing with Docker
 -----------------------------------
 
 First, install `Docker <https://docs.docker.com/get-docker/>`_ for your OS. If running with WSL2, you should still download Docker Desktop for Windows.
 
 To use the latest image, run::
 
-    docker pull samhorsfield96/ggcaller:master
+    docker pull samhorsfield96/ggcaller:latest
 
 To run ggCaller from the Docker Hub image, run::
 
-	cd test && docker run --rm -it -v $(pwd):/workdir -v $(pwd):/data samhorsfield96/ggcaller:master ggcaller --balrog-db /app/ggc_db --refs /workdir/pneumo_CL_group2_docker.txt --out /workdir/ggc_out
+	cd test && docker run --rm -it -v $(pwd):/workdir -v $(pwd):/data samhorsfield96/ggcaller:latest ggcaller --balrog-db /app/ggc_db --refs /workdir/pneumo_CL_group2_docker.txt --out /workdir/ggc_out
 
 You can also build the image yourself. First download and switch to the ggCaller repository::
 
@@ -54,10 +54,6 @@ Once loaded, add the conda bin directory to your path variable and run ggCaller
 Installing with conda
 -----------------------------------
 
-.. important::
-    We are aware of issues installing from conda at the moment.
-    We recommend installing from docker or source at this time.
-
 Installing with conda is the easiest way to get ggCaller up and running, and will install all dependencies.
 
 If you do not have ``conda`` you can install it through

docs/quickstart.rst

@@ -1,10 +1,6 @@
 Quickstart
 ==================================
 
-.. important::
-    We are aware of issues installing from conda version at the moment.
-    We recommend installing via Docker at this time.
-
 Installation
 ------------
 
@@ -45,7 +41,7 @@ To run ggCaller with just reads::
 
 If using Docker, run with the below command, ensuring you keep ``--balrog-db /app/ggc_db`` and ``/workdir`` paths as specified below. Replace ``path to files`` with the absolute path to the directory of files in ``input_docker.txt``::
 
-	docker run --rm -it -v $(pwd):/workdir -v <path to files>:/data samhorsfield96/ggcaller:master ggcaller --balrog-db /app/ggc_db --refs /workdir/input_docker.txt --out /workdir/output_path 
+	docker run --rm -it -v $(pwd):/workdir -v <path to files>:/data samhorsfield96/ggcaller:latest ggcaller --balrog-db /app/ggc_db --refs /workdir/input_docker.txt --out /workdir/output_path 
 
 .. important::
     We haven't extensively tested calling genes within

ggCaller/__init__.py

@@ -2,4 +2,4 @@
 
 '''ggCaller: a gene caller for Bifrost graphs'''
 
-__version__ = '1.3.5'
+__version__ = '1.3.6'

panaroo_runner/generate_output.py

@@ -340,8 +340,8 @@ def generate_GFF(graph, high_scoring_ORFs, input_colours, isolate_names, contig_
                                            .replace(";", " ")],
                     }
                     feature = SeqFeature(
-                        FeatureLocation(entry[1][0][0], entry[1][0][1]),
-                        type="CDS", strand=strand, qualifiers=qualifiers
+                        FeatureLocation(entry[1][0][0], entry[1][0][1], strand=strand),
+                        type="CDS", qualifiers=qualifiers
                     )
                     gff_record.features.append(feature)
                     entry_ID += 1