README.md

pyBWA

Python libraries to interact with BWA mapper

The goal is to make it very easy to run bwa from any python script

Requires

bwa in your environmental PATH

Install

git clone https://github.com/VDBWRAIR/pyBWA.git
python setup.py install

Simple Example

import bwa
import sys

reference_path = sys.argv[1]
read_path = sys.argv[2]

# Ensure reference is indexed
bwa.index_ref( reference_path )

# Setup and run bwa mem
mem = bwa.BWAMem( reference_path, read_path )
retstat = mem.run( 'myoutput.sai' )

# Check return status
if retstat != 0:
    sys.stderr.write( "Error running bwa" )

Multiple reads and references

import bwa
import sys

reference_path = sys.argv[1]
read_path = sys.argv[2]

# If read_path or reference_path are a directory
# they can contain multiple files that will be concatted
# together into a single file.
# Reads can also be .sff files that will be converted to fastq
reads = bwa.compile_reads( read_path )
refs = bwa.compile_refs( reference_path )

# Ensure reference is indexed
bwa.index_ref( refs )

# Setup and run bwa mem
mem = bwa.BWAMem( refs, reads )
retstat = mem.run( 'myoutput.sai' )

# Check return status
if retstat != 0:
    sys.stderr.write( "Error running bwa" )

Executables

pyBWA comes with some utility executables that wrap the functionality of BWA mapping in a single easy to use executable.

• map_bwa.py wraps up bwa mem mapping in an easy to use single executable
  • It utilizes bwa.index_ref, bwa.compile_reads and bwa.compile_refs to easily add SFF files, fastq files and fasta reference files to the mapping
• sai_to_bam converts the output sai sam file to an indexed/sorted bam file