Command line object for HHfilter Multiple Sequence Alignment filtering application
HHfilterCommandline
(cmd=’hhfilter’, **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for HHfilter [1] [2] alignment filter application
https://toolkit.tuebingen.mpg.de/hhfilter
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. |
Examples
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 subprocess
module.