dansondergaard / tmhmm.py Goto Github PK

It would be nice to be able to make poster probability plots as the original TMHMM.

When running the program using a FASTA input file with multiple sequences, all of the output was being directed to the first header. It seems that in your load_fasta_file function of your utils.py script, you forgot a line in your else statement redefining the header. For some reason, without defining a new header, the sequences and annotations were all directed to the first header of the FASTA. Putting a line in the else statement to make a new header (as I did here in line 53) seemed to resolve the issue. Thanks for writing this program!

Best,
Jason

Hi,

Thanks for creating this package. However, I am encountering an issue. Running tmhmm -m TMHMM2.0.model -f test.fa, I get the following error message:

/anaconda3/lib/python3.6/site-packages/tmhmm/init.py:21: RuntimeWarning: divide by zero encountered in log
_, path = viterbi(sequence, *model)

Any insights/help would be greatly appreciated!

Thanks,
Paulina

Maybe just let the user do this, it's pretty easy with joblib.

This previously was working for me, but it is still possible i am doing something wrong.

I am using: annotation,pos_memb=tmhmm.predict(fasta,'TMHMM.model'), as I iterate through a list of FASTA sequences.

I am (now) getting the following error:
"TypeError: predict() missing 1 required positional argument: 'model_or_filelike'"

Any tips would be appreciated.

Traceback (most recent call last):
  File "./annotate_with_hmms.py", line 180, in <module>
    main()
  File "./annotate_with_hmms.py", line 48, in main
    annotator.find_tms()
  File "./annotate_with_hmms.py", line 121, in find_tms
    locations = self.run_tmhmm(gb)
  File "./annotate_with_hmms.py", line 125, in run_tmhmm
    annotation, posterior = tmhmm.predict(str(gb.seq), 'TMHMM2.0.model')
TypeError: predict() missing 1 required positional argument: 'model_or_filelike'

By the way, str(gb.seq) is just protein sequence, not a fasta file name.

Hi @dansondergaard ,

I've set up a clean env to install your tool and installing just your package works, but execution results in this error

Traceback (most recent call last):
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 581, in _build_master
    ws.require(__requires__)
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 898, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 789, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.15.4 (/home/ibis/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages), Requirement.parse('numpy<1.14.0,>=1.9.2'), {'scikit-bio'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/bin/tmhmm", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3126, in <module>
    @_call_aside
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3110, in _call_aside
    f(*args, **kwargs)
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3139, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 583, in _build_master
    return cls._build_from_requirements(__requires__)
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 596, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "/home/pgsb/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages/pkg_resources/__init__.py", line 789, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.15.4 (/home/ibis/daniel.lang/anaconda3/envs/membrane/lib/python3.6/site-packages), Requirement.parse('numpy<1.14.0,>=1.9.2'), {'scikit-bio'})

Forcing downgrading to numpy==1.13.0 solves the problem.

pip install numpy==1.13.0

Easy fix would be to adjust the yml...

Thanks for sharing this nice tool - finally an open-source implementation 👍

Best,
Daniel

Hello, sorry but I have to ask as a beginer:

If trying to use tmhmm.py as a library in Python 3.8.2:
import tmhmm
annotation, posterior = tmhmm.predict(sequence, 'mymodel.model')

I do not know how to use it

• especialy "mymodel.model".

I tried TMHMM2.model file getting:
"TypeError: predict() missing 1 required positional argument: "model_or_filelike"

Shall I use "TMHMM1.0.model" or "PDBseqs.fasta"?

Could you give me some advice, please?

Thank you very much.

Petr Adamek

Dear dansondergaard,
first congratulation you developed such a good software,I have installed it.if I used the test.fa,it will work successful ,But If I used a protein with a "U" in sequence,it doesn't work and produce a error.
but if I put this protein with "U" in TMHMM website,it will work and produce a prediction result. can you help how to solve this problem?

Hi,

I am getting this error.

command: tmhmm -f test.fa -m /TMHMM2.0.model
Traceback (most recent call last):
File "/usr/local/bin/tmhmm", line 10, in
sys.exit(cli())
File "/usr/local/lib/python3.7/dist-packages/tmhmm/cli.py", line 77, in cli
for entry in load_fasta_file(args.sequence_file):
File "/usr/local/lib/python3.7/dist-packages/tmhmm/utils.py", line 52, in load_fasta_file
append_entry(header, sequence_parts, entries)
File "/usr/local/lib/python3.7/dist-packages/tmhmm/utils.py", line 38, in append_entry
id, description = header.split(None, 1)
ValueError: not enough values to unpack (expected 2, got 1)