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wdecoster/getNMtag.py

Last active April 14, 2017 13:07
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getNMtag.py
import pysam
def extractNMFromBam(bam):
'''
loop over a bam file and get the edit distance to the reference genome
stored in the NM tag
scale by aligned read length
'''
samfile = pysam.AlignmentFile(bam, "rb")
return [read.get_tag("NM")/read.query_alignment_length for read in samfile.fetch()]
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