[Bioperl-l] SeqIO

[Jason Stajich]

probably you should try specifying the format explicitly first- as in  
(-format => 'gcg')

-j
On Mar 5, 2008, at 6:22 PM, Chris Fields wrote:

> I thought GCG format changed somewhere along the way but I maybe  
> I'm wrong?  Regardless, you'll have to post this as a bug (along  
> with an example file).
>
> Also, kind of odd that the sequence data wasn't checked...
>
> chris
>
> On Mar 5, 2008, at 5:43 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
>> CCCCTAGGAGCTCAGTGGGCTGGTT51GGATTCCGTGCCATCCCGGCAGGGCAGAGCCTCGGGAGGGGG 
>> CGAAGGT
>> T101GCCCGGGGCCGTGCGCTGGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCC151TGCGGTTGCAGC 
>> GGCTGCT
>> GGGGTTGCGCGTGGAAACCGCGCCCCGCACT201TGCGGCGGGCGAGCCCATCGCGCCGTAGTACAGGT 
>> GCAGAGC
>> GCTGGGGG251GCGCCAGGATCCCCGGCATCGCAGGGCCCGAGGGGTCCGGCCCCACTCGC301ATGGG 
>> GCCAGCG
>> GGCGGCTCTACGGACACTGCATAGTCCGAGACTGGAGC351GTAAGTGTAGGTGCCGGCCGCCGGGCAG 
>> TCCCCTG
>> GCAGCGGGGCTGCAA401AGAAAGCCGGGTCCTGCTCCACGCCATCCAGCGGGGATGTGTCCGGAGTG4 
>> 51GGCAG
>> AGGGTAGCCGTCGAGCGCGGGAGCGCCCAGTCCCTGGCAGTCCCG501ATAGTGGGGGCCCATGTGCGG 
>> AGACATC
>> AGCGGAGGACCGGCCGGATAGC551CCGGCTCCGGGAAAGGCAGACCCAGGCCATCCATGGCCACGCGG 
>> CCGCCC6
>> 01TCGGGACCAAGCGCGCCGGCCTGGGGCTCGACGAGAGCGTGCAGGAAGCC651TCCCTCCACCCGCT 
>> TCATGCG
>> CTTCACCTGCTTGCGCCGCCGCGGCCGGT701ACTTGTAGTTGGGGTGGTCCTGCATATGCTGCACGCG 
>> CAGCCGC
>> TCGGCC751TCTTCCACGAAGGGCCGCTTCTCTGCCAAGGTCAACGCCTTCCAAGACTT801GCCTGCA 
>> GGG
>>
>>
>>
>> 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
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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