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
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 thesubprocess
module.