AUTHOR
Luis M. Rodriguez-R < lmrodriguezr at gmail dot com >
DESCRIPTION
This script is the core of the VNTRs analysis tool (http://bioinfo-prod.mpl.ird.fr/xantho/utils/#vntrs). It requires the vntrs.bme file, at the examples folder. Run it with no arguments to check the required parameters.
LICENSE
This script is distributed under the terms of The Artistic License. See LICENSE.txt for details.
SYNOPSIS
perl polloc_vntrs.pl arguments
The arguments must be in the following order:
- Configuration
-
The configuration file (a .bme or .cfg file).
- Output
-
Output base, a path to the prefix of the files to be created.
- Build groups
-
Any non-empty string to create groups of loci, or empty string to avoid grouping. If empty (
''), extension and summary are ignored. - Extend groups
-
Any non-empty string to extend the groups, or empty string to avoid extension.
- Summarize groups
-
Any non-empty string to produce additional summaries per group, or empty string to avoid summaries.
- Names
-
The identifiers (names) of the input genomes in a single string separated by colons (
:). Alternatively, use an empty string ('') to use names based on the filename. - Inseqs
-
All the following arguments will be treated as input files. Each file is assumed to contain a genome (that can contain one or more sequence) in [multi-]fasta format.
Run perl polloc_vntrs.pl without arguments to see the help message.