Add the read group ID to each read name in a BAM or SAM file.

add_rgid_to_qname.py

"""Add the read group ID to each read name in a BAM or SAM file.

Must output to SAM format to get the header.

To directly convert to BAM, pipe to samtools view:

python add_rgid_to_qname.py INPUT.sam /dev/stdout | samtools view -Sb /dev/stdin > OUTPUT.bam

"""

import pysam

def main():
    import argparse
    
    parser = argparse.ArgumentParser(description="Add read group ID to the read name (qname).")
    
    parser.add_argument('input_file', help="SAM/BAM input file.")
    parser.add_argument('output_file', help="SAM output file.")
    
    opts = parser.parse_args()
    
    if opts.input_file.endswith(".sam"):
        input_file = pysam.Samfile(opts.input_file, "r")
    elif opts.input_file.endswith(".bam"):
        input_file = pysam.Samfile(opts.input_file, "rb")
    else:
        raise IOError, "Input not a sam or bam file."
    
    assert opts.output_file.endswith(".sam"), "Can only output to SAM format."
    output_file = pysam.Samfile(opts.output_file, "wh", template=input_file)
    
    for read in input_file.fetch():
        read_tags = dict(read.tags)
        read_RGID = str(read_tags['RG'])
        read.qname = "%s_%s" % (read_RGID, read.qname)
        output_file.write(read)
    
    input_file.close()
    output_file.close()

if __name__ == "__main__":
    main()