[Bioperl-l] Parsing Hit/Query Frames from Blastx

[Jason Stajich]

See the FAQ.

http://bioperl.org/Core/Latest/faq.html#Q3.5

On Nov 26, 2004, at 1:52 PM, davila wrote:

> Hi,
>
> Trying to parse a Blasxt output file, I realized it is not catching  
> the real values of Hit_Frame and Query_Frame such as showed in the  
> Bioperl Howtos:
>
> http://bioperl.org/HOWTOs/SearchIO/use.html
>
> HSP  	frame  	0  	$hsp->query->frame,$hsp->hit->frame
>
> My code (listed below) is returning wrong (Hit and Query) Frame  
> values, maybe I am doing something wrong. Any help would be greatly  
> appreciated.
>
> Thanks, Alberto
>
> *******
>
> Code:
>
> use lib "/usr/local/bioperl14";
> use Bio::SearchIO;
>
>
>   $searchio = new Bio::SearchIO ('-format' => 'blast',
>                                  '-file'   => 'clusters.blast');
>
>   while ($result = $searchio->next_result) {
>      $query_name = $result->query_name();
>      $cluster_id = $query_name;
> print "$cluster_id\n";
>      $rank = 1;
>      while ($hit = $result->next_hit) {
>        ($gi) = $hit->name =~ /gi\|(\d+)\|/;
>        $hsp = $hit->next_hsp;
>        $hit_length=$hit->length;
> #        $query_frame = $hsp->query->frame,$hsp->hit->frame;
>        $query_frame = $hsp->query->frame;
> print "$query_frame\n";
>        $hit_frame = $hsp->hit->frame;
> print "$hit_frame\n";
>        $hsp_query_string = $hsp->query_string;
> #print "$hsp_query_string\n\n";
>        $hsp_homology_string = $hsp->homology_string;
> #print "$hsp_homology_string\n\n";
>        $hsp_hit_string = $hsp->hit_string;
> #print "$hsp_hit_string\n\n";
>         $hsp_frac_identical =$hsp->frac_identical*100;
> #print "$hsp_frac_identical%\n\n";
>         $hsp_frac_conserved= $hsp->frac_conserved*100;
> #print "$hsp_frac_conserved%\n\n";
> $hsp_align="$hsp_query_string\n$hsp_homology_string\n$hsp_hit_string";
>
> print "$hsp_align\n\n\n\n";
>                                 }
>                 }
>
> Results:
>
> [root at genome blast]# perl align-teste1.pl
> Name "main::gi" used only once: possible typo at align-teste1.pl line  
> 17.
> Name "main::hsp_frac_conserved" used only once: possible typo at  
> align-teste1.pl line 33.
> Name "main::hit_length" used only once: possible typo at  
> align-teste1.pl line 19.
> Name "main::hsp_frac_identical" used only once: possible typo at  
> align-teste1.pl line 31.
> Name "main::rank" used only once: possible typo at align-teste1.pl  
> line 15.
> 333
> 334
> 335
> 336
> 337
> 1 (should be +2)
> 0 (should be -1)
> YLTPTPIEPHL
> Y+TPTPIEPHL
> YITPTPIEPHL
>
>
>
> 338
> 339
> 340
> 341
> 342
> 343
> 0 (should be +1)
> 0 (should be +1)
> IHCEELKQLGRASEKCVL*LFNYSLDTGQVPAKWRHGIIVPQLKPNKSANSMASFRPAPKHSKLNRLGVPL 
> LA
> ++ E L+ LG  +   VL LFN SL TG VP  W+ G+I+P LK  K A  + S+RP    S L ++    
> ++A
> LYNEALQHLGITALNVVLRLFNESLRTGVVPPAWKTGVIIPILKAGKKAEDLDSYRPVTLTSCLCKVMERI 
> IA
>
>
>
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/