NAME

inst-abbr-ids.pl - Abbreviate seq ids in FASTA files (optimized)

VERSION

version 0.242020

USAGE

inst-abbr-ids.pl <infiles> --id-regex=<str> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input FASTA files [repeatable argument].

--id-regex=<str>

Regular expression for capturing the original seq id.

The argument value can be either a predefined regex or a custom regex given on the command line (do not forget to escape the special chars then). The following predefined regexes are available (assuming a leading '>'):

- :DEF (first stretch of non-whitespace chars)
- :GI  (number nnn in  gi|nnn|...)
- :GNL (string xxx in gnl|yyy|xxx)
- :JGI (number nnn in jgi|xxx|nnn or jgi|xxx|nnn|yyy)
- :PAC (number nnn in xxx|PACid:nnn)

OPTIONAL ARGUMENTS

--outdir=<dir>

Optional output dir that will contain the abbreviated FASTA files (will be created if needed) [default: none]. Otherwise, output files are in the same directory as input files.

--id-prefix-mapper=<file>

Path to an optional IDM file explicitly listing the infile => prefix pairs. Useful in the context of processing multiple input files. This argument and the next one (--id-prefix) can be both specified together. In such a case, however, a single pipe char is appended to the combined prefix.

--id-prefix=<str>

String to use as the seq id prefix (e.g., NCBI taxon id, 4-letter code) [default: none].

--store-id-mapper

Store the IDM file corresponding to each output file [default: no].

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Valerian LUPO <valerian.lupo@doct.uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.