NAME

cdhit-tax-filter.pl - # CONTRIBUTOR: Valerian LUPO <valerian.lupo@uliege.be>

VERSION

version 0.252830

NAME

cdhit-tax-filter.pl -

VERSION

version

USAGE

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

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

OPTIONAL ARGUMENTS

--identity=<n>

--filter=<file>

Path to an IDL file specifying the taxonomic filter to be applied. This requires a local mirror of the NCBI Taxonomy database [default: none].

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

--keep-all

Extract all the sequences of the specified taxa from the clusters instead of using only the longest (when possible) [default: no].

--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

--store-id-mapper

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

--out[-suffix]=<suffix>

Suffix to append to infile basenames for deriving outfile names [default: none]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Valerian LUPO <valerian.lupo@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.