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Sequencing pipeline

Project description


Execute as follows:

$ python --help
Usage: seqpipe [OPTIONS]

  Create read-genome matrix and compute all read alignments. Subsequently,
  apply various scripts and aggregate results.

  -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


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 * * Various helper methods * * Plot various statistics


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


Run tests using:

$ tox

Release package

This guide assumes a properly setup ~/.pypirc.

Build package:

$ python 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 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.


Create dev-builds with:

$ pip install --user -e .

Project details

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