[Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Feb 5 14:52:18 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2445





------- Comment #7 from cjfields at uiuc.edu  2008-02-05 14:52 EST -------
(In reply to comment #6)
> With the new SearchIO.pm and blast.pm from SVN the parsing is different.
> However $hit->score and $hit->raw_score do not return values.
> $hit_bits does work.
> 
> while (my $result = $in->next_result ) {
>         while ( my $hit = $result->next_hit) {
>                         print $hit->name, "\t";
>                         print $hit->bits, "\t";
>                         print $hit->significance, "\n"; 
>         }
> 

(In reply to comment #6)
> With the new SearchIO.pm and blast.pm from SVN the parsing is different.
> However $hit->score and $hit->raw_score do not return values.
> $hit_bits does work.
> 
> while (my $result = $in->next_result ) {
>         while ( my $hit = $result->next_hit) {
>                         print $hit->name, "\t";
>                         print $hit->bits, "\t";
>                         print $hit->significance, "\n"; 
>         }

In general with complex fixes like this it's better to grab the whole
distribution just in case.  You'll have to at least replace
Bio::Search::HSP::GenericHSP, Bio::Search::Hit::GenericHit, and
Bio::SearchIO::SearchResultEventBuilder on top of what you already have, though
there may be others.


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