Bio-MUST-Core
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bin/extract-ali.pl view on Meta::CPAN
#!/usr/bin/env perl
# PODNAME: extract-ali.pl
# ABSTRACT: Extract sequences from a FASTA database file based on id lists
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);
use aliased 'Bio::MUST::Core::Ali::Stash';
use aliased 'Bio::MUST::Core::IdList';
my %args;
$args{truncate_ids} = 1 if $ARGV_truncate_ids;
# load database
my $db = Stash->load($ARGV_database, \%args);
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $list = IdList->load($infile);
# assemble Ali and store it as FASTA file
my $ali = $ARGV_reorder ? $list->reordered_ali($db)
: $list->filtered_ali($db)
;
$ali->dont_guess;
my $outfile = change_suffix($infile, '.ali');
$ali->store($outfile);
}
__END__
=pod
=head1 NAME
extract-ali.pl - Extract sequences from a FASTA database file based on id lists
=head1 VERSION
version 0.240390
=head1 USAGE
extract-ali.pl <infiles> --database=<file> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item <infiles>
Path to input IDL files [repeatable argument].
=for Euclid: infiles.type: readable
repeatable
=item --database=<file>
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