[Bioperl-l] bioperl capability

[deequan]

Howdy there,  

         Yes, quite right.  I apologize for the double posting.  Moreover, I
appreciate your assistance in trying to sort out what can and cannot be done
with bioperl.  To address the problem previously stated, I put together a
remarkably misbehaving script that has the following parts:

#Some parsing:
         $q_start = $hsp->query->start;
         $q_end = $hsp->query->end;
         $h_start = $hsp->hit->start;
         $h_end = $hsp->hit->end;
         $length = $hsp->query->seqlength();
         $id = $hit->accession;		
		
          print OUT "$id\t"; 	
          my $seq;
          if($h_start<$h_end){

#the bit per your recommendation		
		my $begin = $h_start-$q_start+1;
		my $cease = ($length - $q_end) + $h_end; 
		my $strand = 1;
		my $factory = Bio::DB::GenBank->new(-format=> 'genbank',
			-seq_start =>$begin,
			-seq_stop =>$cease,
			-strand => $strand, #1 = plus, 2 = minus
		);
		$seq = $factory->get_Seq_by_acc($id);
	}else{#else assume backward, code not shown}

#and some stuff to retrieve the sequence

	my $len = $seq->length();
	my $string = $seq->subseq(1, $len);
	print OUT "length = $len\t";
	print OUT "seq = $string\n";


In your previous reply, you said the code accessing the seq object created
by get_Seq_by_acc would have to pass that obj (here $seq) to a seqIO for
basic IO purposes.  Not seeing exactly how to go about that, I tried some
other functions in combination that seemed as though they should work
(length() and subseq()).  Unfortunately, the program does not even run to
that point, as the script throws an exception:

------------- EXCEPTION -------------
MSG: acc CP000948 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:18
2
STACK toplevel test.pl:36
-------------------------------------


Oddly, the record corresponding to this accession number can be found here:
http://www.ncbi.nlm.nih.gov/nuccore/169887498

Perhaps you'd be willing to offer another hint.  Thank you for your
assistance thus far.  And on behalf of all posters, thank you for sharing
your knowledge.  'Preciate.

David Q.


Chris Fields-5 wrote:
> 
> I think I already answered this:
> 
> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/20302/focus=20305
> 
> chris
> 
> 

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