secretome_pipe_3.0.py 文件源码

def signalp():
    singleline()
    command = ("signalp3.0 -t euk -short -m hmm " + path + "singleline.fasta | grep ' S ' > " + path + "signalpOUT.txt")
    print "\nRunning SignalP"
    signalpRUN = subprocess.check_call([command], shell=True)
    print "SignalP Complete"

    # Generate the list of sequences with siganal peptides using the mature sequences

    print "\nCreating SignalP protein list"
    command_list = ("cut -d ' ' -f 1 " + path + "signalpOUT.txt")
    file_out4 = open(path + "goodlistSigP.txt", "w")
    tab = subprocess.check_call([command_list], stdout=file_out4, shell=True)
    file_out4.close()

# This function creates a fasta file containing the complete sequences with signal peptides