[Bioperl-l] remoteblast result in text format

[Damien Mattei]

Thanks Mathieu,it works well now.


> Wiepert, Mathieu wrote:
> 
>> Hi,
>>
>> Just saw this, sorry for the delay.  If you look at the synopsis for 
>> RemoteBlast, you can see how to save the output.  What I sent you 
>> earlier was not what I finally put in.  You have my alpha code ;-)  So 
>> parseBlastObject() is garbage.  I have cut and pasted the synopsis 
>> into a script, and it executed (assuming it can find the test amino.fa 
>> file, and I see there is a problem with the way I have the 
>> $result->query_name(), keeps returning me a reference not the string 
>> name,

yes i noticed too that it return HASH ref or something like but it 
shouldn't be hard to fix in your code.
Another thing i don't understand is the use of the $v variable in your 
program as this variable seems to remain unchanged :


>>
>> This is what I just ran...
>>
>> #!/usr/bin/perl -w
>> use Bio::Tools::Run::RemoteBlast;
>> use strict;
>> my $prog = 'blastp';
>> my $db   = 'swissprot';
>> my $e_val= '1e-10';
>> my @params = ( '-prog' => $prog,
>>        '-data' => $db,
>>        '-expect' => $e_val,        '-readmethod' => 'SearchIO' );
>>
>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>
>> #change a paramter
>> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens 
>> [ORGN]';
>>
>> #remove a parameter
>> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>>
>> my $v = 1;

ok for init

>> my $str = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 'fasta' );
>>  while (my $input = $str->next_seq()){
>>   #Blast a sequence against a database:
>>     #Alternatively, you could  pass in a file with many    #sequences 
>> rather than loop through sequence one at a time
>>   #Remove the loop starting 'while (my $input = $str->next_seq())'
>>   #and swap the two lines below for an example of that.
>>   my $r = $factory->submit_blast($input);
>>   #my $r = $factory->submit_blast('amino.fa');
>>   print STDERR "waiting..." if( $v > 0 );

tested here

>>   while ( my @rids = $factory->each_rid ) {
>>     foreach my $rid ( @rids ) {
>>       my $rc = $factory->retrieve_blast($rid);
>>       if( !ref($rc) ) {
>>         if( $rc < 0 ) {
>>           $factory->remove_rid($rid);
>>         }
>>         print STDERR "." if ( $v > 0 );

tested again

>>         sleep 5;
>>       } else {         my $result = $rc->next_result();
>>         #save the output
>>         my $filename = $result->query_name()."\.out";
>>         $factory->save_output($filename);
>>         $factory->remove_rid($rid);
>>         print "\nQuery Name: ", $result->query_name(), "\n";
>>         while ( my $hit = $result->next_hit ) {
>>           next unless ( $v > 0);

tested, $v is never modified in the program

>>           print "\thit name is ", $hit->name, "\n";
>>           while( my $hsp = $hit->next_hsp ) {
>>             print "\t\tscore is ", $hsp->score, "\n";
>>           }         }
>>       }
>>     }
>>   }
>> }
>>


Damien.


----------------------------
Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
mailto:mattei@unice.fr
http://www-iag.unice.fr/
----------------------------