format_converter.pl

#! /usr/bin/perl

# Universal? bioperl format converter

use strict; use warnings;
use Bio::SeqIO;
use Getopt::Long;

my $usage = "format_converter.pl --in-file <input_file> --in-format <input_file_format>  --out-file <output_file>  --out-format <output_file_format>\n";
my $in_file;
my $in_format;
my $out_file;
my $out_format;

GetOptions(
            'in-file=s'  => \$in_file,
            'in-format=s'  => \$in_format,
            'out-file=s'   => \$out_file,
            'out-format=s' => \$out_format,
) or die $usage;

my $seq_in = Bio::SeqIO->new( -file => "<$in_file",
                              -format => $in_format, );
                                
my $seq_out = Bio::SeqIO->new( -file => ">$out_file",
                               -format => $out_format, );
                                 
while ( my $inseq = $seq_in->next_seq ) 
{
	$seq_out->write_seq($inseq);
}