[Bioperl-l] SeqIO

[Staffa, Nick (NIH/NIEHS)]

So the Howto says that Bio::SeqIO will read almost any known format
including GCG. 
So I create a GCG file with Seqlab and try to printout its sequence as a
string. ( I did guess at the way to get the sequence string:

#!/usr/bin/perl -w
use strict;
$| = 1;
use Bio::SeqIO;
my $number_of_files = @ARGV;
if(!$number_of_files){print "no files entered\n";exit:}
foreach my $file (@ARGV){
my $seqio_object = Bio::SeqIO->new(-file => $file);
my $seq_object = $seqio_object->next_seq;
my $sequence = $seq_object->seq;
print "$sequence\n";
my $status = &windowscore($sequence);
}

But what it returned was the entire contents of the file with no format
decoding. Have I been deluded?

NewDNALength:810March5,200818:26Type:NCheck:3368..1TGTTCGAATTCCGTGCGGTCCACCT
CCCCTAGGAGCTCAGTGGGCTGGTT51GGATTCCGTGCCATCCCGGCAGGGCAGAGCCTCGGGAGGGGGCGAAGGT
T101GCCCGGGGCCGTGCGCTGGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCC151TGCGGTTGCAGCGGCTGCT
GGGGTTGCGCGTGGAAACCGCGCCCCGCACT201TGCGGCGGGCGAGCCCATCGCGCCGTAGTACAGGTGCAGAGC
GCTGGGGG251GCGCCAGGATCCCCGGCATCGCAGGGCCCGAGGGGTCCGGCCCCACTCGC301ATGGGGCCAGCG
GGCGGCTCTACGGACACTGCATAGTCCGAGACTGGAGC351GTAAGTGTAGGTGCCGGCCGCCGGGCAGTCCCCTG
GCAGCGGGGCTGCAA401AGAAAGCCGGGTCCTGCTCCACGCCATCCAGCGGGGATGTGTCCGGAGTG451GGCAG
AGGGTAGCCGTCGAGCGCGGGAGCGCCCAGTCCCTGGCAGTCCCG501ATAGTGGGGGCCCATGTGCGGAGACATC
AGCGGAGGACCGGCCGGATAGC551CCGGCTCCGGGAAAGGCAGACCCAGGCCATCCATGGCCACGCGGCCGCCC6
01TCGGGACCAAGCGCGCCGGCCTGGGGCTCGACGAGAGCGTGCAGGAAGCC651TCCCTCCACCCGCTTCATGCG
CTTCACCTGCTTGCGCCGCCGCGGCCGGT701ACTTGTAGTTGGGGTGGTCCTGCATATGCTGCACGCGCAGCCGC
TCGGCC751TCTTCCACGAAGGGCCGCTTCTCTGCCAAGGTCAACGCCTTCCAAGACTT801GCCTGCAGGG


 
Nick Staffa 
Telephone: 919-316-4569  (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina