Command line object for HHfilter Multiple Sequence Alignment filtering application
HHfilterCommandLine
(cmd='hhfilter', **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for HHfilter alignment filter application
https://toolkit.tuebingen.mpg.de/hhfilter
Filter an alignment by maximum sequence identity of match states and minimum coverage.
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
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). |