[Bioperl-l] Problem with StandAloneBlastPlus

[Ashton Trey Belew]

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  Hello Dario,
  Below is a portion of a little script which I use for
StandAloneBlast and which uses -m 7.  It doesn't exactly answer your
question, but I hope it will be similar enough to prove helpful.
  My ignorant thought is that you can modify my use of -m to suit your
purpose; but after rereading your message I am guessing you already
tried something similar.
 -Trey

my @params = (-program => 'blastn', -b => $max_hits,
              -I => 't', -a => $processors,
              -database => $library_db, -m => 7,);

my $query_count = 0;
while (my $query_seq = $query_library->next_seq()) {
 $query_count++;
 my $search = new Bio::Tools::Run::StandAloneBlast(
  -_READMETHOD => 'blastxml', @params);
 $search->m(7);
 my $blast_output = new Bio::SearchIO(
  -format => 'blastxml', -verbose => 1,);
 $blast_output = $search->blastall($query_seq,
  -format=>'blastxml', -verbose => 1,);
 my $result_count = 0;
  while (my $result = $blast_output->next_result()) {
  ## Collect alignments
  }  ## End of results by query
}  ## End of queries


On 07/21/2014 11:57 AM, Darío Carballido wrote:
> Hello,
> 
> 
> 
> I’m working with this script that uses StandAloneBlastPlus, and I
> would like to take advantage of a new feature in the latest
> releases of blast+, which allows me to present the query coverage
> in the output (among other values). For that to work, the value of
> –outfmt needs to be quoted (for example, -outfmt “7 std qcovs”), so
> I’m passing the outfmt parameter via
> 
> 
> 
> -method_args => [ '-outfmt' => '"7 std qcovs"' ]
> 
> 
> 
> (I’m using single quotes with doubles inside, so that the double
> quotes are passed literally).
> 
> 
> 
> But when I run it, the quotes seem to get lost and I end up with
> the error I get when I pass that value without the quotes:
> 
> 
> 
> Error: Too many positional arguments (1), the offending value: std
> 
> 
> 
> 
> I have tried lots of combinations with single, double quotes,
> character escaping and I couldn’t find the way to make it work.
> 
> 
> 
> Any help?
> 
> 
> 
> Thanks,
> 
> Darío Carballido
> 
> 
> 
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> list Bioperl-l at mailman.open-bio.org 
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> 
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