Samwell: a python package for using genomic files... well

Samwell provides elegant utilities for managing biological data.

Quickstart

First install samwell:

pip install samwell

Reading/Writing BAMs with automatic inference of filetype

Samwell provides easy utilities for reading/writing BAMs:

from samwell import sam
with sam.writer("my-output-file.bam") as out_bam:
    with sam.reader("myfile.bam") as in_bam:
        for read in fp:
            if read.is_paired:
                out_bam.write(read)

Realigning fastqs with bwa

You can use samwell to easily realign fastq records as necessary

from samwell import sam
from samwell import bwa_mem
with sam.reader("myfile.bam") as in_bam:
    with sam.writer("outfile.bam") as out_bam:
        fastq_gen = (FastqRecord.build(read) for read in in_bam)
        gen = clip_specific_reads(fastq_gen)
        out_bam.write(bwa_mem.align(gen))

See samwell.bwa_mem module for more detail.

Developing with samwell

Samwell uses poetry for dependency managment.

Please install poetry using the instructions in the above link. Then simply execute:

poetry install

Checking the Build

Linting

poetry run flake8 --config=flake8.cfg samwell

Type Checking

poetry run mypy -p samwell --config=mypy.ini

Unit Tests

poetry run python -m pytest --cov=samwell --cov-branch

nh13 / samwell