Package: seqpipe
RNAseq Analysis Pipeline========================|PyPI| |Build Status|Installation------------Install ``seqpipe`` using ``pip``:.. code:: bash$ pip install seqpipe``seqpipe`` offers various commandline-arguments:::$ seqpipe --helpUsage: seqpipe [OPTIONS] COMMAND [ARGS]...Options:--help  Show this message and exit.Commands:mapstatsIn particular, the mapping pipeline is interesting:.. code:: bash$ seqpipe map --helpUsage: seqpipe map [OPTIONS]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.Usage-----To map a directory of reads to two references, execute it as follows:.. code:: bash$ seqpipe map \-r seqpipe/tests/data/reads/ \-g seqpipe/tests/data/references/10-ref.fa \-g seqpipe/tests/data/references/20-ref.fa \-o my_mappingThis will create a ``my_mapping`` directory which contains twodirectories: \* ``runs`` stores all data related to each individual readfile \* ``results`` contains data generated by scripts from the``scripts`` folderAn overview of the read distributions can then be generated via:.. code:: bash$ seqpipe stats plot_rdist -o my_images/ my_mapping/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 sequentialpipeline \* ``plot_expression_differences.py`` \* visualize differencesin RNAseq expression levels over pairs of samplesLinks------  `Github <https://github.com/kpj/SeqPipe>`__-  `PyPi <https://pypi.python.org/pypi/seqpipe>`__Dependencies------------Tools: \* cutadapt \* fastqc \* `moreinfo <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/>`__\* bowtie \* samtools \*`specifications <https://samtools.github.io/hts-specs/SAMv1.pdf>`__ \*bedtoolsLanguages: \* bash \* python \* numpy \* pandas \* seaborn \* matplotlib\* tqdm \* biopython \* pysam \* joblib \* click \* sh \* coloramaDevelopment notes-----------------Tests~~~~~Run tests using:.. code:: bash$ toxRelease package~~~~~~~~~~~~~~~This guide assumes a properly setup ``~/.pypirc``.Build package:.. code:: bash$ python setup.py sdistRegister it (only once):.. code:: bash$ twine register dist/seqpipe-X.Y.Z.tar.gzTry installation locally:.. code:: bash$ 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 --helpTry installation using test-servers:.. code:: bash$ twine upload -r test dist/seqpipe-X.Y.Z.tar.gz$ pip install -i https://testpypi.python.org/pypi seqpipe$ seqpipe --helpCheck `testpypi-page <https://testpypi.python.org/pypi/seqpipe>`__.Finally, install it on actual server:.. code:: bash$ twine upload dist/seqpipe-X.Y.Z.tar.gz$ pip install -U seqpipe$ seqpipe --helpCheck actual `pypi-page <https://pypi.python.org/pypi/seqpipe>`__.Misc~~~~Create dev-builds with:.. code:: bash$ pip install --user -e .Run uninstalled version:.. code:: bash$ python -m seqpipe.mainEnable bash-autocompletion as follows:.. code:: bash$ _SEQPIPE_COMPLETE=source seqpipe >> ~/.bashrc$ . ~/.bashrc.. |PyPI| image:: https://img.shields.io/pypi/v/seqpipe.svg?style=flat:target:.. |Build Status| image:: https://travis-ci.org/kpj/SeqPipe.svg?branch=master:target: https://travis-ci.org/kpj/SeqPipe