hmm-profile 0.0.2

Hidden Markov Model profile tools (reader/writer/data structures)

HMM_profile

Hidden Markov Model profile toolkit.

Written in the base of HMMER User's Guide.

Usage

With my package you can read and write hmm profile files. It's easy to use and easy to read - the best documentation is a well-written code itself, so don't be scared about reading source code.

I decided to use an already opened file as a function parameter, due to file can come from different places, not only local drive.

For a writer's functions, I decided to use local file. But you can use an underlying function to get file content directly without saving to file.

Reader

Read all hmm from file

The read_all function returns generator to optimise memory usage - it's a common pattern that one file contains many models.

from hmm_profile import reader


with open('/your/hmm/profile/file.hmm') as f:
    model_generator = reader.read_all(f)  # IMPORTANT: returns generator

models = list(model_generator)

Read single model

If you have only single model files, you can use this method. It will return models.HMM ready to use.

from hmm_profile import reader


with open('/your/hmm/profile/file.hmm') as f:
    model = reader.read_single(f) 

Writer

Write multiple models to single file

from hmm_profile import writer

models = [...]
path = '/your/hmm/profile/file.hmm'

writer.save_many_to_file(hmms=models, output=path)

Write single model to file

from hmm_profile import writer

model = ...
path = '/your/hmm/profile/file.hmm'

writer.save_to_file(hmm=model, output=path)

Get file content without saving

from hmm_profile import writer

model = ...

lines = writer.get_lines(model)  # IMPORTANT: returns generator
content = ''.join(lines)

Support/bugs

If you have a file that is not readable or has some glitches on save, please crate the issue and attach this file. Bug reports without files (or good examples if you can't provide full file) will be ignored.

Guarantees

In the near future, I will implement the periodic task, that will be testing if all hmm profiles from Pfam are readable and writable without errors.