NAME
tax-filter-ali.pl - Apply a taxonomic filter to ALI files
VERSION
version 0.242020
USAGE
tax-filter-ali.pl --filter=<file> --taxdir=<dir> <infiles>
[optional arguments]
REQUIRED ARGUMENTS
- <infiles>
-
Path to input ALI 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
- --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>
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.