Joachim Bargsten > Bio-Gonzales > fasta-grep

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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

--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>

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