[Bioperl-l] More on EUtilities problem

Warren Gallin wgallin at ualberta.ca
Mon Oct 22 20:28:55 EDT 2007


I seem to be missing something here.

I took the code from the HOWTO as a template and wrote the following  
code snippet (@gisearch_number is an array of gi numbers, prints out  
as expected and can be used to successfully download the relevant  
records using Batch Entrez):
______________________________________________________________

#Create new EUTILS  history object for submitting a large array of gi  
numbers
     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'epost',
         -db      => 'protein',
         -id      => \@ginumber_search,
         -keep_histories => 1
     );

     my $count = @ginumber_search;


     my $history;
     if ($history = $gpeptfactory -> next_History){
    		print "Posted successfully\n";                            
#Prints as expected for successful history
     	print "WebEnv    : ", $history -> get_webenv,"\n";
     	print "Query_key : ",$history->get_query_key,"\n";
     }
     $file = 'temp_hold.gb';

     $gpeptfactory->set_parameters (-eutil => 'efetch',
     							   -rettype => 'genbank',
     							   -history => $history,
     							
	);
	my ($retmax, $retstart) = (300,0);
	my $retry = 0;
RETRIEVE_SEQS: while ($retstart < $count) {
	
     $gpeptfactory->set_parameters(
     						-retmax => $retmax,
                             -retstart => $retstart,
                             );
     eval{
         $gpeptfactory->get_Response(-file => $file);
         print "Output file is $file.\n";
     };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++ && goto RETRIEVE_SEQS;
     }
     else{
     	
     	my $retend = $retstart + $ retmax;
     	print "Loaded entries $retstart through $retend on retry # 
$retry.\n";

     	$retstart += $retmax;
     	$retry = 0;
     }
}

         $retr_seq = Bio::SeqIO->new(
             -file   => $file,
             -format => 'genbank'
         );

________________________________________________
At this point the program fails because there is no file written.

It appears that the get_Response method is not doing its thing.

Also, on each iteration of the loop enclosing the eval the first pass  
fails with the following error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:177
-----------------------------------------------------------
  and then the second pass evaluates as correct - but the output file  
is never opened or written to.

I've tried to pass $file,  "$file" , ">>$file"  and a literal string  
of a file name, with and without the >>, but to no avail.

So I think that I must be missing something basic here, but I am  
unable to see what.

Any advice would be most welcome.

Warren Gallin




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