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Id: 36216
Status: rejected
Priority: 0/
Queue: bioperl

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Owner: Nobody in particular
Requestors: kashi.mail [...] gmail.com
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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 ====================================================================
From: cjfields [...] uiuc.edu
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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 > > > ====================================================================
No response.
No response. Rejecting ticket; I can't replicate the issue.


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