[Bioperl-l] strange problem

Chris Fields cjfields at uiuc.edu
Thu Mar 22 11:30:28 EDT 2007


This is a bug.  Could you add this to bugzilla with a representative  
report and script?  It should be easy to fix as it's likely just a  
regex problem.

http://www.bioperl.org/wiki/Bugs
http://bugzilla.open-bio.org/

chris

On Mar 22, 2007, at 9:11 AM, Patricia Rodriguez Tome wrote:

> Hi
>
> I have found a parsing problem in  SearchIO
> I have this result:
>
>                                                                   
> Score    E
> Sequences producing significant alignments:                       
> (bits) Value
>
> UniRef50_Q9X0H5 Cluster: Histidyl-tRNA synthetase; n=4;  
> Thermoto...    23     650
>
>
>
> I do a very simple parsing with SearchIO
> my $in = new Bio::SearchIO(-format => 'blast',
>                            -file => $ARGV[0]);
>
> while (my $hit = $result->next_hit()) {
>   print "name\t", $hit->name, "\n";
>   print "length\t", $hit->length, "\n";
>   print "accession\t", $hit->accession, "\n";
>   print "description\t", $hit->description, "\n";
>   print "raw_score\t", $hit->raw_score, "\n";
>   print "significance\t", $hit->significance, "\n";
>   print "bits\t", $hit->bits, "\n";
>
> And the result is:
> name    UniRef50_Q9X0H5
> length  420
> accession       UniRef50_Q9X0H5
> description     Cluster: Histidyl-tRNA synthetase; n=4;
> Thermotogaceae|Rep: Histidyl-tRNA synthetase - Thermotoga maritima
> raw_score       ...
> significance    23
> bits    22.7
>
> As you see the three dots at the end of description get into the raw
> score instead, then the evalue gets the raw score
> I am using bioperl1.5.1 and tried even with 1.5.2 but get the same  
> result
> Where can I change it ?
>
> Grazie
>
> Patricia
>
> -- 
> Dr. Patricia Rodriguez-Tomé, PhD
> CRS4 - Bioinformatics
> Loc. Pixina Manna Edificio 3
> Pula 09010 (CA), Italy
> http://www.bioinformatica.crs4.org
>
>
>
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> Bioperl-l at lists.open-bio.org
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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