Command line object for HHblits Multiple Sequence Alignment application
HHblitsCommandLine
(cmd='hhblits', **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for HHblits [1] [2] alignment generation
https://toolkit.tuebingen.mpg.de/hhblits
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. |
Examples
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.
Attributes
parameters |
Methods
__call__ ([stdin, stdout, stderr, cwd, env]) |
Executes the command, waits for it to finish, and returns output. |
set_parameter (name[, value]) |
Set a commandline option for a program (OBSOLETE). |