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

[Charles Hauser]

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