meme-get-motif

Usage:

meme-get-motif [options]

Description

Extract specified motifs from a MEME text (.txt) format file.

Input

The program reads a file in MEME format from standard input.

Output

The program writes a MEME text format file to standard output.

Options

Option Parameter Description Default Behavior
General Options
-idmotif id Extract the motif with ID motif id. This switch may be repeated. Outputs nothing.
-a Check the alternate ID instead of the ID of the motif for matches in conjunction with the -id option. (The alternate ID is the first word, if any, occurring after the ID on the MOTIF line in the MEME .txt file.) Only the motif with the given ID is used.
-ia Check both the alternate ID and the ID of the motif for matches in conjunction with the -id option. Only the motif with the given ID is used.
-all Extract all the motifs in the given file. Extract only the motifs with the specified IDs.
-rc Reverse-complement each extracted motif before outputing. This requires a complementable alphabet. Do not reverse-complement the motifs.