secretome_pipe_3.0.py 文件源码

def tmhmm():
    command = ("tmhmm -short " + path + "signalP_pass.fasta")
    file_out = open(path + "tmhmmOUT.txt", "w")
    print "\nRunning tmhmm on mature signalp sequences only"
    tmhmmRUN = subprocess.check_call([command], stdout=file_out, shell=True)
    file_out.close()
    print "tmhmm complete"
    print "\nIdentifying sequences without tm regions."
    # This section of code parses the output from tmhmm and collects fastas with no TM regions
    openfile = open(path + "tmhmmOUT.txt", "r")
    file_out2 = open(path + "tmhmmGoodlist.txt", "a")
    for line in openfile:
        if "\tPredHel=0\t" in line:
            goodname = line.partition('\t')[0] + '\n'
            file_out2.write(goodname)
    openfile.close()
    file_out2.close()

#This function uses targetp to verify the destination of the signal peptide
#NOTE for plant networks use -P over -N