—#!/usr/bin/env perl
# PODNAME: app-len-ids-ali.pl
# ABSTRACT: Appends seq lengths to ids in ALI files (as SCaFoS)
use
autodie;
use
Smart::Comments;
use
Bio::MUST::Core;
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 0.181180
=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