[Bioperl-l] SearchIO Parse Errors

Brandon Barker brandon.barker at gmail.com
Fri Mar 23 02:46:06 EDT 2007


Hi,

I'm using Bioperl to run BLAST and parse the results of many pairs of
sequences.  Some of these pairs work fine, but for some of the others
my script outputs errors of the following form:


Bio::SearchIO::blast=HASH(0x1a18040)parse error on F18G5.3 / CBG16182
Bio::SearchIO::blast=HASH(0x19ff2cc)parse error on Y73E7A.3 / CBG22266
Bio::SearchIO::blast=HASH(0x1a0cbe4)parse error on T23F1.6 / CBG24659
Bio::SearchIO::blast=HASH(0x19fcca8)parse error on Y71G10AR.4 / CBG13872


The last two words on the lines above are the sequences that are
trying to be being aligned.  I'm using the following code to construct
the searchio objects:


  my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

  $factory->outfile('blast.out');
  my $report = $factory->bl2seq($input, $input2);
  try {
  my $result = $report->next_result;
   .....
  }

If it would be helpful, I would be more than happy to make an archive
of the two sequence files and the bioperl script.  I searched the
bioperl core codebase briefly but didn't see anything that looked
familiar to this problem.

Thanks in advance,


-- 
Brandon Barker
Phone: (859) 948-5335


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