phe.mapping.BWAMapper module

Implementation of the Mapper class using BWA (Heng Li) mapper.

Date:17 Sep, 2015 Author:Alex Jironkin

class BWAMapper(cmd_options=None)

Bases: phe.mapping.Mapper

BWA mapper developed by Heng Li.

Methods

get_samtools_version()	Get version of samtools used.
make_bam(*args, **kwargs)	Make indexed BAM from reference, and fastq files.
validate()	Validate itself, by checking appropriate commands can run.

create_aux_files
get_info
get_meta
get_version
make_sam

create_aux_files(ref)

Create required auxiliary files for ref.

Parameters:

ref: str

Path to the reference file.

Returns:

bool:

True if auxiliary files were created, False otherwise.

get_info(plain=False)

Get information about the mapper.

get_version()

Get the version of the underlying command used.

make_sam(*args, **kwargs)

Make SAM from reference, and fastq files.

Parameters:

ref: str

Path to the reference file used for mapping.

R1: str

Path to the R1/Forward reads file in FastQ format.

R2: str:

Path to the R2/Reverse reads file in FastQ format.

out_file: str

Name of the output file where SAM data is written.

sample_name: str

Name of the sample to be included in the read group (RG) field.

make_aux: bool, optional

True/False to make auxilliary files (default: False).

Returns:

bool:

True iff mapping returns 0, False otherwise.

name = 'bwa'

Plain text name of the mapper.