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
-
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>