seqpipe 0.0.4

Sequencing pipeline

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 .