Package: tmhmm.py
IntroductionThis repository houses a Python 3.5+ implementation of transmembrane helix
hidden Markov model (TMHMM) originally
described in:E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.A hidden Markov model for
predicting transmembrane helices in protein sequences. In J. Glasgow,
T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors,
Proceedings of the Sixth International Conference on Intelligent Systems for
Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.Why?I did this for a few reasons:the source code is not available as part of the publication,the downloadable binaries are Linux-only,the downloadable binaries may not be redistributed, so it's not possible to
put them in a Docker image or a VM for other people to use,the need to predict transmembrane helices on a large dataset, which rules
out the web service.This Python implementation includes a parser for the undocumented file format
used to describe the model and a pretty fast Cython implementation of the
Viterbi algorithm used to perform the annotation. The tool will output files
similar to the files produced by the original TMHMM implementation.IncompatibilitiesThe original TMHMM implementation handles ambigious characters and gaps in an
undocumented way. However, tmhmm.py does not attempt to handle such
characters at all and will fail. A possible fix is to replace those
characters with something also based on expert/domain knowledge. For details,
see issue #9.InstallationThis package supports Python 3.5, 3.6, and 3.7. Install with:$ pip install tmhmm.pyOnly Linux is supported at the moment.Usage$ tmhmm -h
  usage: tmhmm [-h] -f SEQUENCE_FILE [-m MODEL_FILE] [-p]

  optional arguments:
    -h, --help            show this help message and exit
    -f SEQUENCE_FILE, --file SEQUENCE_FILE
                          path to file in fasta format with sequences
    -m MODEL_FILE, --model MODEL_FILE
                          path to the model to use
    -p, --plot            plot posterior probabiliesThe-p/--plotoption will only be available ifmatplotlibis installed
and importable.Say we have the following sequence in FASTA format in a file calledtest.fa:>B9DFX7|1B|HMA8_ARATH Copper-transporting ATPase PAA2, chloroplastic  [Arabidopsis thaliana ]
MASNLLRFPLPPPSSLHIRPSKFLVNRCFPRLRRSRIRRHCSRPFFLVSNSVEISTQSFESTESSIESVKSITSDTPIL
LDVSGMMCGGCVARVKSVLMSDDRVASAVVNMLTETAAVKFKPEVEVTADTAESLAKRLTESGFEAKRRVSGMGVAENV
KKWKEMVSKKEDLLVKSRNRVAFAWTLVALCCGSHTSHILHSLGIHIAHGGIWDLLHNSYVKGGLAVGALLGPGRELLF
DGIKAFGKRSPNMNSLVGLGSMAAFSISLISLVNPELEWDASFFDEPVMLLGFVLLGRSLEERAKLQASTDMNELLSLI
STQSRLVITSSDNNTPVDSVLSSDSICINVSVDDIRVGDSLLVLPGETFPVDGSVLAGRSVVDESMLTGESLPVFKEEG
CSVSAGTINWDGPLRIKASSTGSNSTISKIVRMVEDAQGNAAPVQRLADAIAGPFVYTIMSLSAMTFAFWYYVGSHIFP
DVLLNDIAGPDGDALALSLKLAVDVLVVSCPCALGLATPTAILIGTSLGAKRGYLIRGGDVLERLASIDCVALDKTGTL
TEGRPVVSGVASLGYEEQEVLKMAAAVEKTATHPIAKAIVNEAESLNLKTPETRGQLTEPGFGTLAEIDGRFVAVGSLE
WVSDRFLKKNDSSDMVKLESLLDHKLSNTSSTSRYSKTVVYVGREGEGIIGAIAISDCLRQDAEFTVARLQEKGIKTVL
LSGDREGAVATVAKNVGIKSESTNYSLSPEKKFEFISNLQSSGHRVAMVGDGINDAPSLAQADVGIALKIEAQENAASN
AASVILVRNKLSHVVDALSLAQATMSKVYQNLAWAIAYNVISIPIAAGVLLPQYDFAMTPSLSGGLMALSSIFVVSNSL
LLQLHKSETSKNSLWe can then run tmhmm.py on this file using the following command:$ tmhmm -m TMHMM2.0.model -f test.faThis produces a bunch of files. One is the summary:$ cat B9DFX7|1B|HMA8_ARATH.summary
0-444: outside
445-467: transmembrane helix
468-820: inside
821-843: transmembrane helix
844-852: outside
853-870: transmembrane helix
871-882: insideAn annotation in FASTA format:$ cat B9DFX7|1B|HMA8_ARATH.annotation
>B9DFX7|1B|HMA8_ARATH Copper-transporting ATPase PAA2, chloroplastic  [Arabidopsis thaliana ]
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMMMiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooMMMMMMMMMMMMMMMM
MMiiiiiiiiiiiiAnd finally a file containing the posterior probabilities for each label for
plotting.$ cat B9DFX7|1B|HMA8_ARATH.plot
inside membrane outside
0.20341044516 0.0 0.79658955484
0.210104176071 2.77194446172e-08 0.78989579621
0.189291062167 3.11365191554e-08 0.810708906697
0.253334801857 7.17866017044e-07 0.746664480277
0.126185012808 1.34197873962e-05 0.873801567405
...If the-pflag is set a plot in PDF format will also be produced, following
the same naming scheme as the other output files.APIYou can also use tmhmm.py as a library:import tmhmm
annotation, posterior = tmhmm.predict(sequence, 'mymodel.model')This returns the annotation as a string and the posterior probabilities for
each label as a numpy array with shape(len(sequence), 3)where column 0, 1
and 2 corresponds to being inside, transmembrane and outside, respectively.If you don't need the posterior probabilities setcompute_posterior=False,
this will save quite a lot of computation:annotation, posterior = tmhmm.predict(
    sequence, 'mymodel.model', compute_posterior=False
)