[Bioperl-l] [rt.cpan.org #36216] Unable to parse score from BLAST output file

Kashi Revanna via RT bug-bioperl at rt.cpan.org
Tue May 27 13:52:38 EDT 2008


Tue May 27 13:52:36 2008: Request 36216 was acted upon.
Transaction: Ticket created by kajack
       Queue: bioperl
     Subject: Unable to parse score from BLAST output file
   Broken in: (no value)
    Severity: (no value)
       Owner: Nobody
  Requestors: kashi.mail at gmail.com
      Status: new
 Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=36216 >


Hi, 

I think there is a small bug in the Bio::SearchIO module. I am parsing
the BLAST output file using this module. It works great except for one
thing.

I have included a part of the blast outputfile ( I have modified the
lines to fit into this box). Most of the times the score of Sequences
producing significant alignments is in the format of 6.149e+04. This
module picks up only 6 and ignores other digits. 

Can you please look into this for me.

Thank you in advance
Kashi

Attached: The sample Blast output file is here

====================================================================
BLASTN 2.2.15 [Oct-15-2006]

Query= Contig_1011 (31,018 letters)

Database: scaffold_3.fsa 
           84 sequences; 3,615,155 total letters

Searching..................................................done



                                                Score    E
Sequences producing significant alignments:     (bits) Value

Contig_1011                                 6.149e+04   0.0  
Contig_8873                                      2397   0.0  
Contig_1482                                      2042   0.0  
Contig_9461                                      1475   0.0  
Contig_1977                                       339   7e-92

>Contig_1011
          Length = 31018

 Score = 6.149e+04 bits (31018), Expect = 0.0
 Identities = 31018/31018 (100%)
 Strand = Plus / Plus

                                                                         
Query: 1     cttcaacaaacacgtatttctgaatgaaattgtttagagtttgttgaaggtcacgatcag 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1     cttcaacaaacacgtatttctgaatgaaattgtttagagtttgttgaaggtcacgatcag 60

                                                                         
Query: 61   
gctcatagaccagcggtcctgaaagaggattgcctttaagtttgttggaaaaaacgatta 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61   
gctcatagaccagcggtcctgaaagaggattgcctttaagtttgttggaaaaaacgatta 120


====================================================================


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