This script parses TMHMM short output to a full-length topology output.

TMHMM_parser.py

#################################################################
######################## TMHMM Parser ###########################
#################################################################

# Created by: Kevin Leiss
# Last Updated: 14.12.2016
#
# License: Feel free to use the script, but please refer to me if
#          you used it for publication.
#
# Usage: Scroll down to the botton and specify the file-path to your
#        short TMHMM output. Dont forget to write the StdOut to a file.
#
# Example: python3 TMHMM_parser.py > Output.txt
#
# Output info: i = loop inside
#              o = loop outside
#              T = transmembrane helix

def readTMHMMfile(file_path) :
    print('GeneID\tAAlength\texpAA\tFirst60\tpredHel\tTopology')
    with open(file_path, 'r') as tmhFile:

        for line in tmhFile:
            informations = line.split(sep='\t')

            GeneID = informations[0].split(':')[0]

            lenInfo = informations[1].split('=')[1]

            expAA = informations[2].split('=')[1]

            firstSixty = informations[3].split('=')[1]

            predHel = informations[4].split('=')[1]

            topSeq = informations[5].split('=')[1].rstrip()

            #print(topSeq)
            TMHseq = ''

            if len(topSeq) > 1:

                charI = 0
                location = ''
                locTM = ''
                locTM2 = '0'
                toCoord = False
                locTMprev = ''

                for char in topSeq:

                    if char == 'i' or char == 'o' :

                        if toCoord :
                            TMHseq = TMHseq + location * (int(locTM)-int(locTMprev) - 1) + 'T' * ( int(locTM2) - int(locTM) )
                            #print(location + ' ' + locTM + ' ' + locTM2 + ' '  + locTMprev)
                            #print(int('0'))


                        location = char
                        toCoord = False
                        locTMprev = locTM2
                        locTM = ''
                        locTM2 = ''


                    if char in ['1','2','3','4','5','6','7','8','9','0']:
                        if toCoord :
                            locTM2 = locTM2 + char
                        else :
                            locTM = locTM + char

                    if char == '-' :
                        toCoord = True
            else :
                location = topSeq[0]

            TMHseq = TMHseq + (int(lenInfo) - len(TMHseq)) * location
            topSeq = TMHseq

            print(GeneID + '\t' + lenInfo + '\t' + expAA + '\t' + firstSixty + '\t' + predHel + '\t' + topSeq)





if __name__ == '__main__':
    file = '../Data/TMHMM-predictions.txt'  # Specify the file-path here to the TMHMM output

    readTMHMMfile(file)