[Bioperl-l] Fixed the previously reported BLAST query length issue

[Jason Stajich]

I expect that will lose the Database info though
(check $result->database_name)

This should probably work:
Index: Bio/SearchIO/blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blast.pm,v
retrieving revision 1.59
diff -r1.59 blast.pm
447,448c447,452
<            while( defined ($_) && $_ !~ /^\s+$/ ) {
<                chomp;
---
>            while( defined ($_) ) {
>                if( /^Database:/ ) {
> 		   $self->_pushback($_);
> 		   last;
> 	       }
>                chomp;

On Fri, 6 Jun 2003, Matthew Vaughn wrote:

> If anyone cares to try it out, I fixed the bug I mentioned in my
> previous email. The problem is in the module Bio::SearchIO::blast.pm in
> the method next_result.  Change the following line
>
> while( defined ($_) && $_ !~ /^\s+$/ ) {
>
> to
>
> while( defined ($_) && $_ !~ /^Database/ ) {
>
> This seems to fix the issue without breaking other functionality.
>
> Regards,
>
> Matt
>
> --
> Matthew W. Vaughn, Ph.D.
> Cold Spring Harbor Laboratory
> Delbruck Laboratory / Martienssen Group
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
>
> phone: (516) 422-4128
>
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>

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