[Bioperl-l] parse blast-xml output
Jordi Durban
jordi.durban at gmail.com
Wed Jan 18 10:57:03 UTC 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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