conkit.applications.hhfilter module

Command line object for HHfilter Multiple Sequence Alignment filtering application

class HHfilterCommandline(cmd=’hhfilter’, **kwargs)[source]

Bases: Bio.Application.AbstractCommandline

Command line object for HHfilter [1] [2] alignment filter application

Filter an alignment by maximum sequence identity of match states and minimum coverage.

[1]Alva V., Nam SZ., Söding J., Lupas AN. (2016). The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. pii: gkw348.
[2]Remmert M., Biegert A., Hauser A., Söding J. (2011). HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 9(2):173-5.


To generate a Multiple Sequence Alignment, use:

>>> from conkit.applications import HHfilterCommandline
>>> hhfilter_cline = HHfilterCommandline(
...     input='test.a3m', output='test.filtered.a3m'
... )
>>> print(hhfilter_cline)
hhfilter -i test.a3m -o test.filtered.a3m

You would typically run the command line with hhfilter_cline() or via the Python subprocess module.




__call__([stdin, stdout, stderr, cwd, env]) Execute command, wait for it to finish, return (stdout, stderr).
set_parameter(name[, value]) Set a commandline option for a program (OBSOLETE).