[Bioperl-l] SeqIO

[Staffa, Nick (NIH/NIEHS)]

Verily,
One interpretation of the docs might be: will read any format if the format
is specified.
I was hoping that I could write a program that one needn't specify format.
It'd be more user-friendly and useful.


On 3/5/08 9:33 PM, "Jason Stajich" <jason at bioperl.org> wrote:

> 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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>