[Bioperl-l] Error when parsing a blast file

[Fields, Christopher J]

Try updating to the latest CPAN release (1.6.901, which is the pre-1.7 release).

chris

On Sep 8, 2011, at 1:19 PM, Jeff S Kittrell wrote:

> chris,
> 
> I am using version 1.6.1
> 
> Thanks,
> 
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> <graycol.gif>"Fields, Christopher J" ---09/08/2011 12:28:56 PM---What version of bioperl are you using? I think this issue was addressed a while ago, but it's possi
> 
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> From:
> <ecblank.gif>
> "Fields, Christopher J" <cjfields at illinois.edu>
> <ecblank.gif>
> To:
> <ecblank.gif>
> Jeff S Kittrell <jskittrell at unmc.edu>
> <ecblank.gif>
> Cc:
> <ecblank.gif>
> "<bioperl-l at lists.open-bio.org> " <bioperl-l at lists.open-bio.org>
> <ecblank.gif>
> Date:
> <ecblank.gif>
> 09/08/2011 12:28 PM
> <ecblank.gif>
> Subject:
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> Re: [Bioperl-l] Error when parsing a blast file
> 
> 
> 
> What version of bioperl are you using? I think this issue was addressed a while ago, but it's possible there has been a regression.
> 
> chris
> 
> On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:
> 
> > Hello Gentlemen,
> > 
> > I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> > When the SearchIO parser encounters this record it dies with the error
> > 
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: no data for midline Query ------------------------------------------------------------
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> > STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> > STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> > -----------------------------------------------------------
> > 
> > 
> > Has anyone encountered this problem before? Am I doing something wrong?
> > 
> > Thanks
> > 
> > Jeff Kittrell
> > Department of Genetics, Cell Biology & Anatomy
> > University of Nebraska Medical Center
> > 985805 Nebraska Medical Center
> > Omaha, NE 68198-5805
> > 
> > Query= 78065535
> > 
> > Length=523
> > Score E
> > Sequences producing significant alignments: (Bits) Value
> > 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> > 
> > 
> > > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> > receptor 123 (GPR123), mRNA
> > Length=4298
> > 
> > Score = 576 bits (638), Expect = 1e-163
> > Identities = 466/583 (80%), Gaps = 82/583 (14%)
> > Strand=Plus/Minus
> > 
> > Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> > ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> > Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> > 
> > Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> > |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> > Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> > 
> > Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> > |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> > Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> > 
> > Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> > ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> > Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> > 
> > Query ------------------------------------------------------------ 
> > 
> > Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> > 
> > Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> > |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> > Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> > 
> > Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> > ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> > Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> > 
> > Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> > |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> > Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> > 
> > Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> > ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> > Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> > 
> > Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> > ||||||||||||||||||||||||||||||| ||| || ||||
> > Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> > 
> > 
> > 
> > Lambda K H
> > 0.634 0.408 0.912 
> > 
> > Gapped
> > Lambda K H
> > 0.625 0.410 0.780 
> > 
> > Effective search space used: 47712920310
> > 
> > 
> > 
> > 
> > 
> > 
> > 
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> 
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