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‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.idea
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work
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.nextflow*
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output

‎.gitlab-ci.yml

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image: openjdk:11.0.10-jre-buster
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before_script:
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- java -version
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- apt-get update && apt-get --assume-yes install wget make procps
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- wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
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- nextflow help
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- wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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- mkdir /root/.conda
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- bash Miniconda3-latest-Linux-x86_64.sh -b && cp /root/miniconda3/bin/* /usr/local/bin/
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- rm -f Miniconda3-latest-Linux-x86_64.sh
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- conda --version
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- conda env create -f environment.yml --name bam2tensor_env
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- conda init bash
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- source ~/.bashrc
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- conda activate bam2tensor_env
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test_aligner:
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script:
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- python tests/test_aligner.py
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test_aligner_utils:
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script:
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- python tests/test_aligner_utils.py
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test_intermediate_matrices:
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script:
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- python tests/test_intermediary_matrices.py
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#stages:
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# - test
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#
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#test:
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# stage: test
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# script:
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# - make

‎LICENSE

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Copyright (c) 2023 TRON gGmbH
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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:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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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.

‎MANIFEST.in

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graft src
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graft tests
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prune scripts
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recursive-include docs/source *.py
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recursive-include docs/source *.rst
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include docs/Makefile
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global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
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exclude .bumpversion.cfg .flake8 .travis.yml
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include README.rst LICENSE tox.ini

‎Makefile

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all : clean test check
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clean:
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rm -rf output
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rm -f .nextflow.log*
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rm -rf .nextflow*
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test:
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nextflow main.nf --help
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nextflow main.nf -profile test,conda --output output/test1
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‎README.md

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# bam2tensor
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Toolbox to convert BAM files into tensors
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## Installation
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Download this repository, go to the directory it resides and run:
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```
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git clone https://github.com/TRON-Bioinformatics/bam2tensor.git
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cd bam2tensor
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pip install -e .
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```
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## Requirements
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* Python 3.9+
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* Packages listed under environment.yml
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* The required libraries can be found under `setup.cfg` and are automatically installed when you install this package as shown above.
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## Running the nextflow pipeline
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### Usage:
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```
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nextflow run tron-bioinformatics/bam2tensor
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-profile conda \
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--input_files input_files \
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--publish_dir out_dir \
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--reference genome_ref.fa \
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--window 150 \
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--max_coverage 500 \
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--read_length 50 \
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--max_mapq 60 \
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--max_baseq 82
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```
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### Input:
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* input_files: the path to a tab-separated values file containing in each row the sample name and a BAM file
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The input file does not have a header!
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Example input file:
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name1 tumor_bam1 tumor_bai1 normal_bam1 normal_bai1 candidates1.tsv
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name2 tumor_bam2 tumor_bai2 normal_bam2 normal_bai2 candidates2.tsv
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* reference: the reference genome
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* window: length of the window to be included around the variant
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* max_coverage: Maximum coverage value to normalize coverage matrices
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* read_length: The length of majority of the reads in BAM
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* max_mapq: Maximum mapping quality to normalize mapping quality matrices, values indicating unknown mapping quality is ignored
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* max_baseq: Maximum base quality to normalize base quality matrices, values indicating unknown base quality is ignored
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### Optional input:
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* publish_dir: the folder where to publish output
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* memory: the ammount of memory used by each job (default: 15g)
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* cpus: the number of CPUs used by each job (default: 8)
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### Output:
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* Tensors under the output folder
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‎environment.yml

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name: bam2tensor
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channels:
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- defaults
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- conda-forge
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- bioconda
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dependencies:
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- python=3.9.*
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- conda-forge::cxx-compiler
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- conda-forge::zlib
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- bioconda::samtools
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- bioconda::bedtools
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- bioconda::bcftools
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- pip
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- pip:
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- torch==2.0.1
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- fire==0.5.0
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- pybedtools==0.9.0
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- pysam
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- matplotlib==3.7.1
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- numpy==1.24.3
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- pandas==1.5.3
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- seaborn==0.12.2
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