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Sequencing pipeline

Project description

RNAseq Analysis Pipeline

|PyPI| |Build Status|


Install ``seqpipe`` using ``pip``:

.. code:: bash

$ pip install seqpipe

``seqpipe`` offers various commandline-arguments:


$ seqpipe --help
Usage: seqpipe [OPTIONS] COMMAND [ARGS]...

--help Show this message and exit.


In particular, the mapping pipeline is interesting:

.. code:: bash

$ seqpipe map --help
Usage: seqpipe map [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.


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/


Additional useful scripts are contained in ``extra``. The entry point is
```` (check ``python ./extra/ --help`` for help).

The respective individual files are: \* ```` \*
map length-filtered reads against multiple genomes in succession \*
```` \* visualize data obtained from sequential
pipeline \* ```` \* visualize differences
in RNAseq expression levels over pairs of samples


- `Github <>`__
- `PyPi <>`__


Tools: \* cutadapt \* fastqc \* `more
info <>`__
\* bowtie \* samtools \*
`specifications <>`__ \*

Languages: \* bash \* python \* numpy \* pandas \* seaborn \* matplotlib
\* tqdm \* biopython \* pysam \* joblib \* click \* sh \* colorama

Development notes


Run tests using:

.. code:: bash

$ tox

Release package

This guide assumes a properly setup ``~/.pypirc``.

Build package:

.. code:: bash

$ python 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 seqpipe
$ seqpipe --help

Check `testpypi-page <>`__.

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 <>`__.


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

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