Bio-MUST-Core
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bin/fasta2ali.pl view on Meta::CPAN
#!/usr/bin/env perl
# PODNAME: fasta2ali.pl
# ABSTRACT: Convert FASTA files to 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);
use aliased 'Bio::MUST::Core::Ali';
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $ali = Ali->load($infile);
$ali->dont_guess if $ARGV_noguessing;
$ali->degap_seqs if $ARGV_degap;
my $outfile = change_suffix($infile, '.ali');
$ali->store($outfile);
}
__END__
=pod
=head1 NAME
fasta2ali.pl - Convert FASTA files to ALI files
=head1 VERSION
version 0.240390
=head1 USAGE
fasta2ali.pl <infiles> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item <infiles>
Path to input FASTA files [repeatable argument].
=for Euclid: infiles.type: readable
repeatable
=back
=head1 OPTIONAL ARGUMENTS
=over
=item --degap
Discard gaps when converting sequences [default: no].
=item --[no]guessing
[Don't] guess whether sequences are aligned or not [default: yes].
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