#!/usr/bin/env perl
# PODNAME: stock2ali.pl
# ABSTRACT: Convert STOCKHOLM files to ALI files
use Modern::Perl '2011';
use autodie;
use Getopt::Euclid qw(:vars);
use Bio::MUST::Core::Utils qw(change_suffix);
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $ali = Ali->load_stockholm($infile);
my $outfile = change_suffix($infile, '.ali');
$ali->store($outfile);
}
__END__
=pod
=head1 NAME
stock2ali.pl - Convert STOCKHOLM files to ALI files
=head1 VERSION
version 0.173460
=head1 USAGE
stock2ali.pl <infiles> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item <infiles>
Path to input STOCKHOLM files [repeatable argument].
=for Euclid: infiles.type: readable
repeatable
=back
=head1 OPTIONAL ARGUMENTS
=over
=item --version
=item --usage
=item --help
=item --man
Print the usual program information
=back
=head1 AUTHOR
Denis BAURAIN <denis.baurain@uliege.be>
=head1 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.
=cut