def count_reads_matching_intervals(bam_filename, intervals_filename,
output_filename, logger):
"""
Count number of reads matching the given intervals
filename, which could be a BED or a GFF.
Output the resulting file (a BED) to output filename.
"""
if not os.path.isfile(intervals_filename):
logger.critical("Cannot find exons file %s" % (output_filename))
return None
# intersect BAM with merged exons, outputting one line per
# read that overlaps any region in the merged exons BED
output_filename = get_reads_matching_regions(bam_filename,
intervals_filename,
output_filename, logger)
if output_filename is None:
logger.warning("Cannot access matching regions file %s" \
%(output_filename))
return 0
if not os.path.isfile(output_filename):
logger.warning("Matching regions file %s does not exist" \
%(output_filename))
return None
num_reads = utils.count_lines(output_filename)
return num_reads
def count_reads_matching_intervals(bam_filename, intervals_filename, output_filename, logger):
"""
Count number of reads matching the given intervals
filename, which could be a BED or a GFF.
Output the resulting file (a BED) to output filename.
"""
if not os.path.isfile(intervals_filename):
logger.critical("Cannot find exons file %s" % (output_filename))
return None
# intersect BAM with merged exons, outputting one line per
# read that overlaps any region in the merged exons BED
output_filename = get_reads_matching_regions(bam_filename, intervals_filename, output_filename, logger)
if output_filename is None:
logger.warning("Cannot access matching regions file %s" % (output_filename))
return 0
if not os.path.isfile(output_filename):
logger.warning("Matching regions file %s does not exist" % (output_filename))
return None
num_reads = utils.count_lines(output_filename)
return num_reads
def count_reads_matching_intervals(bam_filename,
intervals_filename,
output_filename):
"""
Count number of reads matching the given intervals
filename, which could be a BED or a GFF.
Output the resulting file (a BED) to output filename.
"""
if not os.path.isfile(intervals_filename):
print "WARNING: Cannot find exons file %s" %(output_filename)
return None
# intersect BAM with merged exons, outputting one line per read that
# overlaps any region in the merged exons BED
intersect_bam_with_bed(bam_filename,
intervals_filename,
output_filename)
if not os.path.isfile(output_filename):
return None
num_reads = utils.count_lines(output_filename)
return num_reads