[Bioperl-l] exonerate (cigar line) to GFF

[Jason Stajich]

mostly because it was expecting you to have provided a whole exonerate
report to have the Target: and Query: lines so you can get the description
line from both query and subject.

But I've updated the exonerate code in CVS to handle only cigar lines as
well.

-jason

On Thu, 22 May 2003, Charles Hauser wrote:

> All,
>
> I'd like to process the cigar line output from exonerate to generate a
> .gff file to load GBrowse.
>
> The Bio::SearchIO::exonerate module appears set up to deal with the
> cigar output but I get the error below.  If, however I run exonerate w/
> --showalignment the script works.  The module appears to generate hsps
> from the cigar line so I thought the script below should work?
>
>
> Can't use an undefined value as an ARRAY reference at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/SearchResultEventBuilder.pm
> line 261, <FH> line 1.
>
>
> data sample:
>
> cigar: 1112122H11.x1 17 541 + scaffold_802 35537 36061 + 2465 M 463 I 1 M 52 D 1 M 8
>
>
> code excerpt:
>
> my $searchio = new Bio::SearchIO(-fh => \*FH,
> 			         -format => 'exonerate');
>
> while ( my $result = $searchio->next_result() ) {
>     print $result->query_name, "\n";
>     while( my $hit = $result->next_hit ) {
> 	while( my $hsp = $hit->next_hsp ) {
> 	    print $hsp->score,"\n";
> 	}
>     }
> }
>
>
> Charles
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu