Metadata-Version: 1.1
Name: seqpipe
Version: 0.0.6
Summary: Sequencing pipeline
Home-page: https://github.com/kpj/SeqPipe
Author: kpj
Author-email: kpjkpjkpjkpjkpjkpj@gmail.com
License: MIT
Description: RNAseq Analysis Pipeline
        ========================
        
        |PyPI| |Build Status|
        
        Installation
        ------------
        
        Install ``seqpipe`` using ``pip``:
        
        .. code:: bash
        
            $ pip install seqpipe
        
        ``seqpipe`` offers various commandline-arguments:
        
        ::
        
            $ seqpipe --help
            Usage: seqpipe [OPTIONS] COMMAND [ARGS]...
        
            Options:
              --help  Show this message and exit.
        
            Commands:
              map
              stats
        
        .. code:: bash
        
            $ seqpipe map --help
            Usage: 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_mapping
        
        This will create a ``my_mapping`` 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
        
        An 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 sequential
        pipeline \* ``plot_expression_differences.py`` \* visualize differences
        in RNAseq expression levels over pairs of samples
        
        Links
        -----
        
        -  `Github <https://github.com/kpj/SeqPipe>`__
        -  `PyPi <https://pypi.python.org/pypi/seqpipe>`__
        
        Dependencies
        ------------
        
        Tools: \* cutadapt \* fastqc \* `more
        info <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/>`__
        \* bowtie \* samtools \*
        `specifications <https://samtools.github.io/hts-specs/SAMv1.pdf>`__ \*
        bedtools
        
        Languages: \* bash \* python \* numpy \* pandas \* seaborn \* matplotlib
        \* tqdm \* biopython \* pysam \* joblib \* click \* sh \* colorama
        
        Development notes
        -----------------
        
        Tests
        ~~~~~
        
        Run tests using:
        
        .. code:: bash
        
            $ tox
        
        Release package
        ~~~~~~~~~~~~~~~
        
        This guide assumes a properly setup ``~/.pypirc``.
        
        Build package:
        
        .. code:: bash
        
            $ python setup.py sdist
        
        Register it (only once):
        
        .. code:: bash
        
            $ twine register dist/seqpipe-X.Y.Z.tar.gz
        
        Try 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 --help
        
        Try 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 --help
        
        Check `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 --help
        
        Check 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.main
        
        .. |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
        
Keywords: bioinformatics sequencing pipeline alignment mapping
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
