conkit.command_line.conkit_predict module¶

This script provides a simplified contact prediction pipeline. It will take either a sequence or alignment as starting point and predict, analyse and evaluate the final prediction and any intermediate results.

It uses two external programs to perform this task.

• HHblits for Sequence Alignment generation, and
• CCMpred for Direct Coupling Analysis.

* The two programs above need to be installed separately *

add_alignment_args(subparsers)[source]¶

Parser with alignment as starting point

add_default_args(parser)[source]¶

Define default arguments

add_sequence_args(subparsers)[source]¶

Parser with sequence as starting point

main(argl=None)[source]¶

The main routine for conkit-predict functionality

Parameters:	argl : list, tuple, optional A list containing the command line flags