#!/usr/bin/env perl
# PODNAME: app-len-ids-ali.pl
# ABSTRACT: Appends seq lengths to ids in ALI files (as SCaFoS)
use Modern::Perl '2011';
use autodie;
use Getopt::Euclid qw(:vars);
use Bio::MUST::Core::Utils qw(secure_outfile);
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $ali = Ali->load($infile);
$ali->dont_guess if $ARGV_noguessing;
# append seq lengths to ids
my $idm = $ali->len_mapper;
$ali->restore_ids($idm);
my $outfile = secure_outfile($infile, $ARGV_out_suffix);
$ali->store($outfile);
}
__END__
=pod
=head1 NAME
app-len-ids-ali.pl - Appends seq lengths to ids in ALI files (as SCaFoS)
=head1 VERSION
version 0.181000
=head1 USAGE
app-len-ids-ali.pl <infiles> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item <infiles>
Path to input ALI files [repeatable argument].
=for Euclid: infiles.type: readable
repeatable
=back
=head1 OPTIONAL ARGUMENTS
=over
=item --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.
=for Euclid: suffix.type: string
=item --[no]guessing
[Don't] guess whether sequences are aligned or not [default: yes].
=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