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"""compute number of reads/alignments from BAM file
===================================================
This is a benchmarking utility script with limited functionality.
Compute simple flag stats on a BAM-file using
the pysam python interface.
"""
import sys
import pysam
assert len(sys.argv) == 2, "USAGE: {} filename.bam".format(sys.argv[0])
is_paired = 0
is_proper = 0
for read in pysam.AlignmentFile(sys.argv[1], "rb"):
is_paired += read.is_paired
is_proper += read.is_proper_pair
print ("there are alignments of %i paired reads" % is_paired)
print ("there are %i proper paired alignments" % is_proper)
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