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

[Chris Fields via RT]

       Queue: bioperl
 Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=36216 >

Please submit this using the BioPerl bugzilla:

http://bugzilla.open-bio.org/

Attach a full BLAST example to the bug report so we can track it.

On Tue May 27 13:52:36 2008, kajack wrote:
> 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
> 
> 
> ====================================================================