conkit.applications.jackhmmer module

Command line object for Jackhmmer Multiple Sequence Alignment generation

class JackhmmerCommandline(cmd=’jackhmmer’, **kwargs)[source]

Bases: Bio.Application.AbstractCommandline

Command line object for Jackhmmer [1] alignment generation

Jackhmmer is an algorithm that uses iterative searches a protein sequence against a protein sequence database to find sequence homologs.

[1]Johnson L. S., Eddy S. R., Portugaly E. (2010). Hidden Markov Model Speed Heuristic and Iterative HMM Search Procedure. BMC Bioinformatics 11, 431.


To generate a Multiple Sequence Alignment, use:

>>> from conkit.applications import JackhmmerCommandline
>>> jackhmmer_cline = JackhmmerCommandline(
...     input="test.fasta", database="uniref100.fasta"
... )
>>> print(jackhmmer_cline)
jackhmmer test.fasta uniref100.fasta

You would typically run the command line with jackhmmer_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).