Ejemplo n.º 1
0
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()
Ejemplo n.º 2
0
        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))
Ejemplo n.º 3
0
 def RunReader():
     infile = str(e3)
     outfile = str(e4)
     BamReader.BamReader(infile, outfile)