NAME

inst-tax-filter.pl - Apply a taxonomic filter to a (UniProt) FASTA database (optimized)

VERSION

version 0.242020

USAGE

inst-tax-filter.pl <infiles> --filter=<file> --taxdir=<dir>
    [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input FASTA files [repeatable argument].

--filter=<file>

Path to an IDL file specifying the taxonomic filter to be applied.

In a tax_filter, wanted taxa are to be prefixed by a '+' symbol, whereas unwanted taxa are to be prefixed by a '-' symbol. Wanted and unwanted taxa are linked by logical ORs.

An example IDL file follows:

-Viridiplantae
-Opisthokonta
+Ascomycota
+Oomycota

--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

OPTIONAL ARGUMENTS

--id-regex=<str>

Regular expression for capturing org from seq id [default: none].

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 '>'):

- :UNI (UniProt OS= field)

--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.