simulome.py 文件源码

def writeMutationLog():
    if sort_log_by == 1:
        startSort = sorted(mutation_log, key=itemgetter(0))
    else:
        startSort = sorted(mutation_log, key=itemgetter(5))

    print "\tWriting mutation log file: " + mut_log_outfile

    try:
        outfile = open(mut_log_outfile,"w")
        outfile.write("START\tEND\tTYPE\tBEFORE\tAFTER\n")
        for line in startSort:
            outfile.write(str(line[0]) + "\t" + str(line[1]) + "\t" + line[2] + "\t" + line[3] + "\t" + line[4] + "\n")
    except Exception, e:
        print "Error writing mutation log. "
        print e
        sys.exit()
    finally:
        outfile.close()


##############
# writeGenome:  This function will write a provided annotation file and genome file. 
#               The isMut parameter is a flag to modify the filename for mutated variants of the simulated genome.
##############