[Bioperl-l] here's a cool bug!

[Jason Stajich]

[jason at ascona jason]$ perl -mBio::SeqIO -e 'print
$sio=Bio::SeqIO->new(-file => "blah.gb")->next_seq->primary_id,"\n";'

 Bio::Seq::RichSeq=HASH(0x8518394)

So there is no VERSION for the sequence...
VERSION       GI:230940

Is that valid Genbank...

Need to make this loop here a little tighter then I guess
in genbank.pm

	  #Version number
	  elsif( /^VERSION\s+(.+)$/ ) {
	      my ($acc,$gi) = split(' ',$1);
	      if($acc =~ /^\w+\.(\d+)/) {
		  $params{'-version'} = $1;
		  $params{'-seq_version'} = $1;
	      }
	      if($gi && (index($gi,"GI:") == 0)) {
		  $params{'-primary_id'} = substr($gi,3);
	      }
	  }

Any takers...?  Make that regexp a little more greedy for GI: perhaps?

-jason
On Thu, 11 Dec 2003, Mark Wilkinson wrote:

> This bug is an interesting one!  It doesn't happen in all cases, only on
> certain genbank records, like the one attached.  Try this out:
>
> perl -MBio::SeqIO -e '$sio=Bio::SeqIO->new(-file => "blah.gb");
> $s=$sio->next_seq; print $s->primary_id;'
>
> that should lead to some raised eyebrows :-)
>
> M
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu