Command line object for CCMpred contact prediction application
CdhitCommandLine
(cmd='cd-hit', **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for Cd-hit
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik’s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute).
CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.
Examples
>>> from conkit.applications import CdhitCommandLine
>>> cdhit_cline = CdhitCommandLine()
>>> print(cdhit_cline)
You would typically run the command line with cdhit_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). |