Pore_c_py
This package provides Python scripts for working with Pore-C data. It is not intended to be used directly by end uses, but rather as part of our Nextflow workflow wf-pore-c. Hence the terse nature of this documentation.
Installation
A package is available to install through either pip:
pip install pore-c-py
or through conda:
conda install -c nanoporetech pore-c-py
Usage
$ pore-c-py --help
usage: pore_c_py [OPTIONS] COMMAND [ARGS].
Available subcommands are:
digest Digest concatemer sequences into monomers using a restriction enzyme.
annotate Annotate alignments with a "walk", which simply
enumerates the alignment coordinates of the monomers comprising the
concatemer.
Example
The following is indicative use, similar to that performed by wf-pore-c.
INPUT="myreads.bam"
ENZYME="NlaIII"
REF="myref.fasta"
OUTPUT="all"
pore-c-py digest "${INPUT}" "${ENZYME}" \
| samtools fastq -T '*' \
| minimap2 -ay -t 8 -x map-ont "${REF}" - \
| pore-c-py annotate - "${OUTPUT}" --monomers --stdout --summary --chromunity \
| tee "${OUTPUT}.ns.bam" \
| samtools sort --write-index -o "${OUTPUT}.cs.bam" -
samtools index "${OUTPUT}.ns.bam"
The digest program can read its input from standard input, so it can be used with
bamindex in
order to process a subset of a file. This is particularly useful for
distributing the workload on a cluster.
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Metadata
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Release files for pore-c-py 2.1.5
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Release files / pore_c_py-2.1.5.tar.gz
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