[Bioperl-l] While loop - SearchIO for BioPerl
Rytsareva, Inna (I)
IRytsareva at dow.com
Wed Jul 8 19:42:54 UTC 2009
Hello,
I have a follow script to parse the BLAST report:
my $in = Bio::SearchIO->new ( -file =>$out_file,
-format =>'blast') or die $!;
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit)
{
while (my $hsp = $hit->next_hsp) {
$qhit = $hit->name;
$start = $hsp->hit->start;
$end = $hsp->hit->end;
}
} print "Hit= ", $qhit,
",Start = ", $start,
",End = ", $end,"\n";
}
Usually, the report has a number of the same hsp for each hit.
Using "print" command it gives me a hit name, start and end positions
for each hit, except last on. For last one it prints all the hsps.
Something like this:
Hit= gnl|DAS|22386,Start = 7578,End = 7601
Hit= gnl|DAS|25627,Start = 2824,End = 2863
Hit= gnl|DAS|25328,Start = 8864,End = 8887
Hit= gnl|DAS|4890,Start = 1896,End = 1919
Hit= gnl|DAS|12191,Start = 1898,End = 1921
Hit= gnl|DAS|4276,Start = 557,End = 580
Hit= gnl|DAS|12959,Start = 801,End = 824
Hit= gnl|DAS|4092,Start = 2266,End = 2304
Hit= gnl|DAS|19740,Start = 13572,End = 13610
Hit= gnl|DAS|12393,Start = 3901,End = 3924
Hit= gnl|DAS|25687,Start = 10415,End = 10438
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Hit= gnl|DAS|12277,Start = 7410,End = 7433
Where Hit= gnl|DAS|12277,Start = 7410,End = 7433 is the last one.
I don't need these duplicates.
How can I fix that?
Thanks,
Inna Rytsareva
Discovery Information Management
Dow AgroSciences
Indianapolis, IN
317-337-4716
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