[Bioperl-l] strange problem

Patricia Rodriguez Tome prtome at crs4.it
Thu Mar 22 10:11:44 EDT 2007


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 ?



Dr. Patricia Rodriguez-Tomé, PhD
CRS4 - Bioinformatics
Loc. Pixina Manna Edificio 3 
Pula 09010 (CA), Italy

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