Bug #36216 for bioperl: Unable to parse score from BLAST output file

Tue May 27 13:52:36 2008 kashi.mail [...] gmail.com - Ticket created

Subject:

Unable to parse score from BLAST output file

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 Show quoted text

>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 ====================================================================

Tue May 27 14:10:00 2008 cjfields [...] uiuc.edu - Correspondence added

From:

cjfields [...] uiuc.edu

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: Show quoted text

> 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 Show quoted text

> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > Sbjct: 1

cttcaacaaacacgtatttctgaatgaaattgtttagagtttgttgaaggtcacgatcag 60 Show quoted text

> > > Query: 61 > gctcatagaccagcggtcctgaaagaggattgcctttaagtttgttggaaaaaacgatta 120 > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > Sbjct: 61 > gctcatagaccagcggtcctgaaagaggattgcctttaagtttgttggaaaaaacgatta 120 > > > ====================================================================

Tue May 27 14:10:04 2008 The RT System itself - Status changed from 'new' to 'open'

Wed Jan 21 23:43:30 2009 cjfields [...] uiuc.edu - Correspondence added

No response.

Wed Jan 21 23:43:32 2009 cjfields [...] uiuc.edu - Status changed from 'open' to 'stalled'

Thu Apr 16 18:10:17 2009 cjfields [...] uiuc.edu - Correspondence added

No response. Rejecting ticket; I can't replicate the issue.

Thu Apr 16 18:10:18 2009 The RT System itself - Status changed from 'stalled' to 'open'

Thu Apr 16 18:10:19 2009 cjfields [...] uiuc.edu - Status changed from 'open' to 'rejected'