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

Date

Jun 28, 2022

Version

v0.0.4

Samwell provides elegant utilities for managing biological data.

Documentation Contents

• Samwell: a python package for using genomic files… well.
  • Documentation Contents
  • Quickstart
  • Developing with samwell
• API
  • Utility Functions for Manipulating DNA sequences.
  • Functions for Creating Useful Iterators
  • Utility Classes for Querying Overlaps with Genomic Regions
  • Utility Classes and Methods for SAM/BAM
  • Utility methods for running BWA
  • Utility Functions for Soft-Clipping records in SAM/BAM Files
  • Classes for generating SAM and BAM files and records for testing

• Release Notes

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.reader("myfile.bam") as in_bam:
    with sam.writer("my-output-file.bam", header=in_bam.header) as out_bam:
        for read in in_bam:
            if read.is_paired:
                out_bam.write(read)

See sam module for more detail.

Realigning fastqs with bwa

You can use samwell to easily realign fastq records as necessary:

from pathlib import Path
from samwell import sam
from samwell.sam import bwa_mem
from samwell.sam import clipping
from samwell.sam.bwa_mem import FastqRecord
with sam.reader("myfile.bam") as in_bam:
    with sam.writer("outfile.bam", header=in_bam.header) as out_bam:
         fastq_gen = iter(FastqRecord.build(read) for read in in_bam)
         for read in bwa_mem.align(fastq_gen, Path("genome.fasta")):
             out_bam.write(read)

See 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