Bio-MUST-Core
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bin/rest-ids-ali.pl view on Meta::CPAN
#!/usr/bin/env perl
# PODNAME: rest-ids-ali.pl
# ABSTRACT: Change (restore) full seq ids in ALI files
use Modern::Perl '2011';
use autodie;
use Getopt::Euclid qw(:vars);
use Smart::Comments;
use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $ali = Ali->load($infile);
$ali->dont_guess if $ARGV_noguessing;
$infile =~ s/$_//xms for @ARGV_in_strip;
my $idmfile = change_suffix($infile, '.idm');
my $idm = IdMapper->load($idmfile);
### Restoring seq ids from: $idmfile
$ali->restore_ids($idm);
my $outfile = secure_outfile($infile, $ARGV_out_suffix);
$ali->store($outfile);
}
__END__
=pod
=head1 NAME
rest-ids-ali.pl - Change (restore) full seq ids in ALI files
=head1 VERSION
version 0.240390
=head1 USAGE
rest-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
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