[Bioperl-l] parse blast-xml output

Jordi Durban jordi.durban at gmail.com
Wed Jan 18 05:57:03 EST 2012


Hi all!
I'm trying to parse a xml blast output (-m 7 option) in order to get the
best hit (I mean the first one) from each result I got.
I've done:
*
my @files=<*>;
my @files2 = grep (/^454AllContigs.fna.masked*/, @files);
foreach my $blast_report(@files2){
# Get the report
my $searchio = new Bio::SearchIO (-format => 'blastxml',
-file=>$blast_report, -best =>'true');
  while( my $result = $searchio->next_result ) {

       my $query=$result->query_name();
         #~ print @query,"\n"; ##### results quey names
         while (my $hits = $result->next_hit) {
        #~ print $hits,"\n"; ###### the whole of hits
              my $name= $hits->name();
              my $desc = $hits->description();
              print $query."\t".$name."\t".$desc,"\n";

*But it does not work as I get the whole of results from a single query.
What I mean:
contig01181    gi|63794|emb|X03832.1|    Chicken mRNA 3' end for fast
skeletal troponin I (sTnI)
contig01181    gi|110293358|gb|DQ646396.1|    Lama pacos troponin 1 type 2
(Tnni2) mRNA, partial cds
contig01181    gi|298897248|emb|FQ224489.1|    Rattus norvegicus
TL0ACA64YG07 mRNA sequence
contig01181    gi|298892466|emb|FQ217985.1|    Rattus norvegicus
TL0ACA12YG21 mRNA sequence
contig01181    gi|298889559|emb|FQ217454.1|    Rattus norvegicus
TL0ACA25YO07 mRNA sequence
contig01181    gi|298888987|emb|FQ223772.1|    Rattus norvegicus
TL0ACA87YD21 mRNA sequence

I know some perl and I think it is a really newbie question but any help
would be appreciate.
Thanks a lot.
-- 
Jordi


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