[Bioperl-l] While loop - SearchIO for BioPerl

Chris Fields cjfields at illinois.edu
Wed Jul 8 21:08:33 EDT 2009


I'm curious as to what this report looks like.  The example report you  
posted to the gbrowse list had serious issues (different problem, 'No  
midline' error which I replicated); mainly there were no blank lines  
making it pretty much invalid, so the parser had issues with it.   
Example lines from one HSP:

 > gnl|DAS|24699 pDAB101580
           Length = 12942
  Score = 50.1 bits (25), Expect = 5e-06
  Identities = 37/41 (90%)
  Strand = Plus / Plus
Query: 10   ccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 50
             ||||||||||||||| ||| |||||||| ||||| ||||||
Sbjct: 4619 ccaaaaaaaaaaaaagaaagaaaaaaaagaaaaagaaaaaa 4659
  Score = 46.1 bits (23), Expect = 8e-05
  Identities = 35/39 (89%)
  Strand = Plus / Plus
Query: 13   aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 51
             ||||||||||||| ||| |||||||| ||||| ||||||
Sbjct: 4621 aaaaaaaaaaaaagaaagaaaaaaaagaaaaagaaaaaa 4659
  Score = 46.1 bits (23), Expect = 8e-05
  Identities = 35/39 (89%)
  Strand = Plus / Plus
Query: 14   aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 52
             ||||||||||||| ||| |||||||| ||||| ||||||
Sbjct: 4621 aaaaaaaaaaaaagaaagaaaaaaaagaaaaagaaaaaa 4659

...

chris




On Jul 8, 2009, at 2:42 PM, Rytsareva, Inna (I) wrote:

> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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