Command line object for Jackhmmer Multiple Sequence Alignment generation
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. |
Examples
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.
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). |