x2y.pl

#!/bin/perl

use strict;
use Bio::SeqIO;

# get command-line arguments, or die with a usage statement
my $usage         = "x2y.pl infile infileformat outfile outfileformat\n";
my $infile        = shift or die $usage;
my $infileformat  = shift or die $usage;
my $outfile       = shift or die $usage;
my $outfileformat = shift or die $usage;
 
# create one SeqIO object to read in, and another to write out
my $seq_in = Bio::SeqIO->new(
                             -file   => "<$infile",
                             -format => $infileformat,
                             );
my $seq_out = Bio::SeqIO->new(
                              -file   => ">$outfile",
                              -format => $outfileformat,
                              );
 
# write each entry in the input file to the output file
while (my $inseq = $seq_in->next_seq) {
    $seq_out->write_seq($inseq);
}