[Bioperl-l] bitscore and rawscore for blast reports

[Marc Logghe]

Hi,
> Im am trying to parse blast reports using the Bio::SearchIO system. 
> 
> #!/usr/bin/perl
> use strict;
> use Bio::SearchIO;
> my( $blastFile ) = @ARGV;
> my $searchio = new Bio::SearchIO( -file=>$blastFile, 
> -format=>'blast' );
> while( my $result = $searchio->next_result() ){
>     while( my $hit = $result->next_hit() ){
>         while( my $hsp = $hit->next_hsp() ) {
>     

Your hit object is a Bio::Search::Hit::BlastHit object. The methods related to score are inherited from Bio::Search::Hit::GenericHit. So have a look there for info about the methods score() and raw_score().

The score for an individual hsp is also inherited:
Bio::SeqFeature::FeaturePair::hscore
Bio::SeqFeature::SimilarityPair::score

You might also have a look at the tutorial about Bio::SearchIO, especially the overview table showing all available methods (http://bioperl.org/HOWTOs/SearchIO/use.html)

HTH,
Marc