cleanFasta

clean Fasta

Convert files to unix format and convert all characters that are not an A,C,G,T or N to N.

Commands

clean

Remove all job data, not the Moa job itself, note that this must be implemented by the template.

run

Cleanup of a FASTA file (in place!)

Parameters

cf_input_dir

Directory with the sequences to run cleanfasta on

type: directory

default: ``

optional: False

cf_input_extension

input file extension

type: string

default: fasta

optional: True

sed_command

type: string

default: /^>/!s/[^ACGTNacgtn]/N/g

optional: True

miscellaneous

Backend

gnumake

Author

Mark Fiers

Creation date

Wed Nov 10 07:56:48 2010

Modification date

Wed Nov 10 07:56:48 2010