[Bioperl-l] SeqIO

[Brian Osborne]

Nick,

Take a look at the GCG files that are used in the SeqIO tests:

bioperl-live//t/data/test.gcg
bioperl-live//t/data/test_badlf.gcg

Does the file that you created have a format like the format in those  
files? I'm guessing you're going to say 'yes', from the looks of your  
output.

Brian O.


On Mar 5, 2008, at 6:43 PM, Staffa, Nick (NIH/NIEHS) wrote:

> 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
>
>
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