comment on

Hi!
I am using bioperl to parse a blast report. I am having
difficulty parsing only the best hsp(high scoring pair)info
as well as the alignment. I currently can get
the alignment to print(clustalW format) but not the
other info concerning the hsp to an out file.

#!/usr/bin/perl 
use warnings;
use strict;
use Bio::SearchIO;
use Bio::AlignIO;

use strict;

my $out = "C:/Documents and Settings/mydir/Desktop/current/bl2seq/1311
+7_aln.out";
my $dir = 'C:/Documents and Settings/mydir/Desktop/current/bl2seq/';
my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => $dir.'13117_2.out');
while( my $result = $in->next_result ) {
  while( my $hit = $result->next_hit ) {
   while( my $hsp = $hit->next_hsp ) {
     if( $hsp->length('total') > 1000 ) {
      if ( $hsp->percent_identity >= 90 ) {
       if(    $hsp->score ){
        if(     $hsp->gaps ){
         if(  $hsp->expect ){
            print  "Hit= ",    $hit->name, 
                    " Length=",     $hsp->length('total'), 
                    " Score=",        $hsp->score,"\n";
            print "Gaps=",    $hsp->gaps,
                    " Expect=",        $hsp->expect,
                    " Percent_id=", $hsp->percent_identity, "\n";
            my $aln = $hsp->get_aln;
            my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file 
+=> $out);
            $alnIO->write_aln($aln);
        }
       }
      }
     }
    }
   }  
  }
}
__DATA__
Query= 13117 Mus musculus genomic with Cassette inserted
         (10,084 letters)



>13117/13117_fasta.Contig1
          Length = 1453

 Score = 2046 bits (1032), Expect = 0.0
 Identities = 1088/1100 (98%), Gaps = 5/1100 (0%)
 Strand = Plus / Minus

                                                                      
+  
Query: 1001 taggaaccattttttttttttct-gtgtttccttca-tcctgtgactctgccaacc-a
+ac 1057
            ||||||||||||||||||||| | |||||||||||| |||||||||||| |||||| |
+||
Sbjct: 1113 taggaaccatttttttttttttttgtgtttccttcaatcctgtgactctaccaaccca
+ac 1054

                                                                      
+  
Query: 1058 tttctaatccctctacctgcaaactacaaactctggtctgccagcaggttatgaattg
+ta 1117
            |||||||||| ||||||||||||||||||||||||||||||||||||||||| |||| 
+||
Sbjct: 1053 tttctaatccttctacctgcaaactacaaactctggtctgccagcaggttataaattt
+ta 994

                                                                      
+  
Query: 1118 aagaaatttcattatgcttttgtctgcaaaatcccccagttctcagaaacaggg-tta
+aa 1176
            |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
+||
Sbjct: 993  aagaaatttcattatgcttttgtctgcaaaatcccccagttctcagaaacaggggtta
+aa 934

                                                                      
+  
Query: 1177 gccaatgtgtagagaagaatgaacaaaa-tgcagaaatgcagggaatcccagtgcctc
+at 1235
            ||||||| |||||||||||||||||||| |||||||| ||||||||||||||||||||
+||
Sbjct: 933  gccaatgggtagagaagaatgaacaaaaatgcagaaaagcagggaatcccagtgcctc
+at 874

                                                                      
+  
Query: 1236 ggggtgggggtggggtgggagtgcagggtcagcagggaccatccagatgctgggacac
+cc 1295
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 873  ggggtgggggtggggtgggagtgcagggtcagcagggaccatccagatgctgggacac
+cc 814

                                                                      
+  
Query: 1296 ctgtgaaatatcacaccctctctgccccgtgctgtcctggattcaggtcaaactggat
+tt 1355
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 813  ctgtgaaatatcacaccctctctgccccgtgctgtcctggattcaggtcaaactggat
+tt 754

                                                                      
+  
Query: 1356 caatctgcataatttgtcccatttagaagggttgggagagggtgagaacaggagggtg
+aa 1415
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 753  caatctgcataatttgtcccatttagaagggttgggagagggtgagaacaggagggtg
+aa 694

                                                                      
+  
Query: 1416 gactgaggaggggggatagatactccccccatcccaaaggcaggcatgaagtagtggc
+ca 1475
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 693  gactgaggaggggggatagatactccccccatcccaaaggcaggcatgaagtagtggc
+ca 634

                                                                      
+  
Query: 1476 gaggaaaccagagtgaacaggctggagtgaaggctggtagctgctagagagaggaggt
+gg 1535
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 633  gaggaaaccagagtgaacaggctggagtgaaggctggtagctgctagagagaggaggt
+gg 574

                                                                      
+  
Query: 1536 gaccgggaggagcagcaggcttgaaaagcacagggtaattgtcagcccagcactgtag
+gg 1595
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 573  gaccgggaggagcagcaggcttgaaaagcacagggtaattgtcagcccagcactgtag
+gg 514

                                                                      
+  
Query: 1596 ggcaatttagtctacttacccagtggcaagaagtaaaaaaaaagtgggctgtgactta
+aa 1655
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 513  ggcaatttagtctacttacccagtggcaagaagtaaaaaaaaagtgggctgtgactta
+aa 454

                                                                      
+  
Query: 1656 gatcttaagactcactagagagggaggggttagcctgggagtgggaggagggagtgca
+ga 1715
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 453  gatcttaagactcactagagagggaggggttagcctgggagtgggaggagggagtgca
+ga 394

                                                                      
+  
Query: 1716 gtttaggaggagacagagactctggagggtgcaaggaagtgtctttagctgagctggg
+ct 1775
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 393  gtttaggaggagacagagactctggagggtgcaaggaagtgtctttagctgagctggg
+ct 334

                                                                      
+  
Query: 1776 gggctgggacgggaaggtagactgaagctgcctgaactgctcatcccgctgggtctga
+gc 1835
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 333  gggctgggacgggaaggtagactgaagctgcctgaactgctcatcccgctgggtctga
+gc 274

                                                                      
+  
Query: 1836 tcccagtggggcggttcgcatgcctggaaggactctaagcaccctcagacctcttact
+ct 1895
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 273  tcccagtggggcggttcgcatgcctggaaggactctaagcaccctcagacctcttact
+ct 214

                                                                      
+  
Query: 1896 gaggttcaagccaatccttcagggtgcttgctgagttggtgacccatctctggaactg
+gt 1955
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 213  gaggttcaagccaatccttcagggtgcttgctgagttggtgacccatctctggaactg
+gt 154

                                                                      
+  
Query: 1956 gtccctgggactcactgcccagcttcacttcattcagcaccatgggtaccgatttaaa
+tg 2015
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 153  gtccctgggactcactgcccagcttcacttcattcagcaccatgggtaccgatttaaa
+tg 94

                                                                      
+  
Query: 2016 atccagtggtcctgcagaggagagattgggagaatcccggtgtgacacagctgaacag
+ac 2075
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||
Sbjct: 93   atccagtggtcctgcagaggagagattgggagaatcccggtgtgacacagctgaacag
+ac 34

                                
Query: 2076 tagccgcccaccctcccttt 2095
            ||||||||||||||||||||
Sbjct: 33   tagccgcccaccctcccttt 14



 Score = 40.1 bits (20), Expect = 1e-005
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                                
Query: 7698 ggggtgggggtggggtggga 7717
            ||||||||||||||||||||
Sbjct: 873  ggggtgggggtggggtggga 854



 Score = 28.2 bits (14), Expect = 0.046
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                          
Query: 8817 catttttttttttt 8830
            ||||||||||||||
Sbjct: 1106 catttttttttttt 1093



 Score = 26.3 bits (13), Expect = 0.18
 Identities = 13/13 (100%)
 Strand = Plus / Plus

                        
Query: 363 cccctccctctct 375
           |||||||||||||
Sbjct: 425 cccctccctctct 437



 Score = 26.3 bits (13), Expect = 0.18
 Identities = 13/13 (100%)
 Strand = Plus / Minus

                         
Query: 7649 agggtgagaacag 7661
            |||||||||||||
Sbjct: 715  agggtgagaacag 703



 Score = 24.3 bits (12), Expect = 0.71
 Identities = 12/12 (100%)
 Strand = Plus / Plus

                        
Query: 5507 cccccctcctca 5518
            ||||||||||||
Sbjct: 679  cccccctcctca 690



 Score = 24.3 bits (12), Expect = 0.71
 Identities = 12/12 (100%)
 Strand = Plus / Minus

                        
Query: 8819 tttttttttttt 8830
            ||||||||||||
Sbjct: 1101 tttttttttttt 1090



 Score = 24.3 bits (12), Expect = 0.71
 Identities = 12/12 (100%)
 Strand = Plus / Minus

                        
Query: 8819 tttttttttttt 8830
            ||||||||||||
Sbjct: 1102 tttttttttttt 1091



 Score = 24.3 bits (12), Expect = 0.71
 Identities = 12/12 (100%)
 Strand = Plus / Minus

                        
Query: 8819 tttttttttttt 8830
            ||||||||||||
Sbjct: 1103 tttttttttttt 1092



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                      
Query: 598 tcctgcagagg 608
           |||||||||||
Sbjct: 84  tcctgcagagg 74



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                       
Query: 4644 gcctgaactgc 4654
            |||||||||||
Sbjct: 304  gcctgaactgc 294



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                       
Query: 4040 ctgcctgaact 4050
            |||||||||||
Sbjct: 306  ctgcctgaact 296



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                       
Query: 9957 ttagctgagct 9967
            |||||||||||
Sbjct: 349  ttagctgagct 339



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 9036 ctgtctcctcc 9046
            |||||||||||
Sbjct: 378  ctgtctcctcc 388



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 7830 tcctcccactc 7840
            |||||||||||
Sbjct: 405  tcctcccactc 415



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                      
Query: 368 ccctctctgcc 378
           |||||||||||
Sbjct: 798 ccctctctgcc 788



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 9047 cccaccccacc 9057
            |||||||||||
Sbjct: 855  cccaccccacc 865



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 9045 cccccacccca 9055
            |||||||||||
Sbjct: 864  cccccacccca 874



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 8608 tttctgagaac 8618
            |||||||||||
Sbjct: 945  tttctgagaac 955



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Plus

                       
Query: 564  aaaaaaaaaat 574
            |||||||||||
Sbjct: 1095 aaaaaaaaaat 1105



 Score = 22.3 bits (11), Expect = 2.8
 Identities = 11/11 (100%)
 Strand = Plus / Minus

                       
Query: 7639 tttgttaagaa 7649
            |||||||||||
Sbjct: 1436 tttgttaagaa 1426


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 1
Number of Hits to DB: 562
Number of extensions: 37
Number of successful extensions: 37
Number of sequences better than 10.0: 1
Number of HSP's gapped: 24
Number of HSP's successfully gapped: 21
Length of query: 10084
Length of database: 1453
Length adjustment: 12
Effective length of query: 10072
Effective length of database: 1441
Effective search space: 14513752
Effective search space used: 14513752
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 11 (22.3 bits)
S2: 11 (22.3 bits)
[download]

I am only interested in parsing out the first hit, which is
the best hit with greater than 98% identity. Any ideas?

In reply to parsing blast output by lomSpace

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