import pysam import pyximport pyximport.install() import _cython_flagstat is_paired, is_proper = _cython_flagstat.count( pysam.AlignmentFile("ex1.bam", "rb")) print ("there are alignments of %i paired reads" % is_paired) print ("there are %i proper paired alignments" % is_proper)
"""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 cython interface. """ import sys import pysam import pyximport pyximport.install() import _cython_flagstat assert len(sys.argv) == 2, "USAGE: {} filename.bam".format(sys.argv[0]) is_paired, is_proper = _cython_flagstat.count( pysam.AlignmentFile(sys.argv[1], "rb")) print ("there are alignments of %i paired reads" % is_paired) print ("there are %i proper paired alignments" % is_proper)
"""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 cython interface. """ import sys import pysam import pyximport pyximport.install() import _cython_flagstat assert len(sys.argv) == 2, "USAGE: {} filename.bam".format(sys.argv[0]) is_paired, is_proper = _cython_flagstat.count( pysam.AlignmentFile(sys.argv[1], "rb")) print("there are alignments of %i paired reads" % is_paired) print("there are %i proper paired alignments" % is_proper)