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Sequencing pipeline

Project 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

In particular, the mapping pipeline is interesting:

.. 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

Enable 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

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