NAME

fasta-grep - grep fasta files

SYNOPSIS

    ./fasta-grep [OPTIONS] [--help] <fasta-file>

DESCRIPTION

find regex in id-header or sequence or specifiy a length condition to select matching fasta sequences. All options, except length, are joined by "or".

To modify the regex to be case insensitive put (?i) in front of it (see also man perlre)

OPTIONS

--only_headers|--oh

Print only fasta headers.

--filter_length <len>

With len '>=', '<=', '>', '==', ...

--filter_id <id_regex>

--filter_seq <seq_regex>

--filter_desc <desc_regex>

--list_ids | -i

Extract the ids of the fasta file

--list_length | -l

Print length and id of every seq

--list_char | -c

Show character distributions for every sequence

--verbose | -v

Print matching ids to STDERR

--print

just print the sequence (use in combination with filter length)

--shift_id <N>

Removes [ID_1] - [ID_N] in fasta header where the header has the form:

    >[ID_1] [ID_2] ... [ID_N] description

--help

Display this msg.

AUTHOR

jw bargsten, <joachim.bargsten at wur.nl>