def main(argv):
try:
opts, args = getopt.getopt(argv, "i:")
except getopt.GetoptError:
usage()
sys.exit(2)
# Get parameters from command line
for opt, arg in opts:
if opt == "-h":
usage()
sys.exit()
elif opt == '-i':
bam_file_name = arg
bam_reader = BamReader(bam_file_name, None)
bam_reader.output_repetitive_reads()
rlen_mean = stats["read_length"]
rlen_sdev = stats["read_length_SD"]
print "mean fragment length taken from config file: %.2f" % (
isize_mean)
print "standard deviation of fragment_length: %.2f" % (isize_sdev)
print "mean read length: %.2f" % (rlen_mean)
print "standard deviation of read length: %.2f" % (rlen_sdev)
else:
# disable this calculation for the time being for the streaming analysis -- require a conf file
# print "error! must supply configuration file of library stats"
# sys.exit(1)
# Get the mean and sdev of insert size from the ORIGINAL bam file
psorted_bam_reader = BamReader(psorted_bamfile_name, output_prefix)
print "calculating mean insert size..."
iterations = 1000000
(isize_mean, isize_sdev, rlen_mean,
rlen_sdev) = psorted_bam_reader.calculate_mean_sdev_isize(iterations)
print "mean fragment length over %d reads: %.2f" % (iterations,
isize_mean)
print "standard deviation of fragment_length: %.2f" % (isize_sdev)
print "mean read length: %.2f" % (rlen_mean)
print "standard deviation of read length: %.2f" % (rlen_sdev)
stats_file = open(output_prefix + ".read_stats.txt", "w")
stats_file.write("fragment_length\t%.2f\n" % (isize_mean))
stats_file.write("fragment_length_SD\t%.2f\n" % (isize_sdev))
stats_file.write("read_length\t%.2f\n" % (rlen_mean))
stats_file.write("read_length_SD\t%.2f" % (rlen_sdev))
def RunReader():
infile = str(e3)
outfile = str(e4)
BamReader.BamReader(infile, outfile)