#!/usr/bin/perl  -w
# This script uses Bio::SeqIO objects
# to convert a Genbank format file to
# a FASTA format file
# Author:  MyName,  12 Oct 2003
# Version 2.0

use strict;
my ($infile, $inSeqIO, $outSeqIO, $seqobj, $accnum);

use Bio::SeqIO;

# Check for filename argument
$infile = $ARGV[0];
if (!defined $infile) {
    die "Usage: $0 inputfile\n";
}

# Create two SeqIO objects:
# one for input
# another for output
$inSeqIO = Bio::SeqIO->new (-file => "$infile", 
                                                -format => 'Genbank');
$outSeqIO = Bio::SeqIO->new (-file=>">$infile.FASTA", 
                                                  -format => 'FASTA');

# In a loop, read each Genbank# sequence, print its 
# accession number  and write it out in FASTA format
while ($seqobj = $inSeqIO->next_seq())  {
      $accnum = $seqobj->accession_number();
      print "Accession#  $accnum\n";
      $outSeqIO->write_seq($seqobj);
}  # End while next_seq()