Sequencing pipeline
Project description
Usage
Execute main.py as follows:
$ python main.py --help Usage: seqpipe [OPTIONS] Create read-genome matrix and compute all read alignments. Subsequently, apply various scripts and aggregate results. Options: -r, --read PATH Path to read file/directory. [required] -g, --genome PATH Path to genome file/directory. [required] -o, --output DIRECTORY Directory to save results to. --scripts / --no-scripts Whether to execute scripts or not. -m, --min-read-len INTEGER Minimal read length. -M, --max-read-len INTEGER Maximal read length. -b, --bowtie-args TEXT Extra arguments for bowtie. -t, --threads INTEGER How many threads to run in. --help Show this message and exit.
This will create a mapping_results_* directory which contains two directories: * runs stores all data related to each individual read file * results contains data generated by scripts from the scripts folder
Extras
Additional useful scripts are contained in extra. The entry point is main.py (check python ./extra/main.py --help for help).
The respective individual files are: * sequential_pipeline.sh * map length-filtered reads against multiple genomes in succession * plot_sequential_data.py * visualize data obtained from sequential pipeline * plot_expression_differences.py * visualize differences in RNAseq expression levels over pairs of samples * utils.py * Various helper methods * mapping_overview.py * Plot various statistics
Dependencies
Tools: * cutadapt * fastqc * more info * bowtie2 * samtools * specifications * bedtools * moreutils
Languages: * bash * python * numpy * pandas * seaborn * matplotlib * tqdm * biopython * pysam * joblib * click * sh * colorama
Development notes
Tests
Run tests using:
$ tox
Release package
This guide assumes a properly setup ~/.pypirc.
Build package:
$ python setup.py sdist
Register it (only once):
$ twine register dist/seqpipe-X.Y.Z.tar.gz
Try installation locally:
$ rm -rf /tmp/seqpipe_tmp
$ virtualenv /tmp/seqpipe_tmp
$ /tmp/seqpipe_tmp/bin/pip install dist/seqpipe-X.Y.Z.tar.gz
$ /tmp/seqpipe_tmp/bin/seqpipe --help
Try installation using test-servers:
$ twine upload -r test dist/seqpipe-X.Y.Z.tar.gz
$ pip install -i https://testpypi.python.org/pypi seqpipe
$ seqpipe --help
Check testpypi-page.
Finally, install it on actual server:
$ twine upload dist/seqpipe-X.Y.Z.tar.gz
$ pip install -U seqpipe
$ seqpipe --help
Check actual pypi-page.
Misc
Create dev-builds with:
$ pip install --user -e .
Project details
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