[Bioperl-l] Arrays of BioSeq and TCoffee

[James Wasmuth]

Thanks to Jason and Brian for solutions, tidy code is so much more, 
errrm... tidy.  ;o)



Jason Stajich wrote:

>On Thu, 16 Jan 2003, James Wasmuth wrote:
>
>  
>
>>Hi people,
>>
>>I have a number of fasta format sequences in one string, which I wish to
>>align using T-Coffee, without writing the sequences to a file first.
>>
>>According to doc for T-Coffee module, the align method will take a
>>filename or an array of references for Bio::Seq objects...
>>
>>I've tried the following script but it fails, I am informed that the
>>first Bio::Seq object contains less than 2 sequences.  Well of course it
>>does, its a Bio::Seq object...  Can anyone see my error...
>>
>>    
>>
>
>  
>
>>my @fasta_seq = qw/  >seq1\nFTTATT  >seq2\nFTTGTT  >seq3\nFTATTT /;
>>my @seq;
>>foreach (@fasta_seq)    {
>>        my $stringfh = new IO::String($_);
>>        my $seqio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta');
>>        push @seq ($seqio_obj->next_seq);
>>    }
>># here I know that @seq is an array of Bio::Seq objects
>>
>>    
>>
>Ye gods, that is scary
>It would seem simplier to me
>
>
>my $fastaseq =<<EOF
>  
>
>>seq1
>>    
>>
>TTACATA
>  
>
>>seq2
>>    
>>
>TGACCAT
>  
>
>>seq3
>>    
>>
>ATAGT
>EOF
>;
>
>my $iostring = new IO::String($fastaseq);
>my $seqio = new Bio::SeqIO(-fh => $stringfh,-format =>'fasta');
>my @seq;
>while( my $seq = $seqio->next_seq) { push @seq,$seq }
>
>
>
>  
>
>>my @params = (some params);
>>my $factory = new Bio::Tools::Run::Alignment::TCoffee (@params);
>>my $aln = $factory->align(@seq);
>>
>>    
>>
>You want an array reference here:
>my $aln = $factory->align(\@seq);
>
>I think this is in the docs though...
>
>  
>
>>Can a Bio::Seq object hold more than one sequence? Is that my problem
>>
>>Many Thanks
>>
>>J
>>
>>
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>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>  
>

-- 

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