conkit.applications.hhblits module

Command line object for HHblits Multiple Sequence Alignment application

class HHblitsCommandline(cmd=’hhblits’, **kwargs)[source]

Bases: Bio.Application.AbstractCommandline

Command line object for HHblits [1] [2] alignment generation

The HHblits program is a homology detection tool by iterative HMM-HMM comparison.

[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 HHblitsCommandline
>>> hhblits_cline = HHblitsCommandline(
...     input="test.fasta", database="uniprot20_29Feb2012"
... )
>>> print(hhblits_cline)
hhblits -i test.fasta -d uniprot20_29Feb2012

You would typically run the command line with hhblits_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).