[Bioperl-l] Bio::Biblio question

[Baranidharan P]

  Dear Mr. Davis

u  can try 
 my @ids= @{ new Bio::Biblio->find ("$gene")->get_all_ids } ;

 foreach my $ids (@ids)
{
print $ids;
}


On Fri, 03 Sep 2004 Sean Davis wrote :
>Dear all,
>
>I have the following code (below) which works in most cases.  However,  sometimes, I get.  The failure is due to a very large result set and  fails at the get_all_ids stage.  I only want the ids and I only want  the first 200 or so.  Is there a way to QUICKLY (ie., without  retrieving the entire XML for each) get only the first 200 ids?
>
>
>my $biblio = Bio::Biblio->new();
>     my $new_biblio=$biblio->find([$gene,$mod]);
>     my $results=$new_biblio->get_count;
>     if ($results) {
>       my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids};
>
>
>------------- EXCEPTION  -------------
>MSG: --- SOAP FAULT ---
>SOAP-ENV:Server Exception from service object: Limit exceeded. Use  iterator instead.
>STACK  Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120] /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:119
>STACK SOAP::Lite::call /Library/Perl/SOAP/Lite.pm:2839
>STACK SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]  /Library/Perl/SOAP/Lite.pm:2802
>STACK Bio::DB::Biblio::soap::get_all_ids  /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:424
>STACK toplevel pubsearch.pl:35
>
>--------------------------------------
>         Bio::Root::Root::throw('Bio::DB::Biblio::soap','-text','---  SOAP FAULT ---\x{a}SOAP-ENV:Server Exception from service obj...')  called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 119
>          Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120]('SOAP::Lite=HASH(0xb8ab08)','SOAP::SOM=HASH(0xd4616c)')  called at /Library/Perl/SOAP/Lite.pm line 2839
>          SOAP::Lite::call('SOAP::Lite=HASH(0xb8ab08)','getAllIDs','SOAP:: Data=HASH(0xd6af78)') called at /Library/Perl/SOAP/Lite.pm line 2802
>          SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]('SOAP:: Lite=HASH(0xb8ab08)','SOAP::Data=HASH(0xd6af78)') called at  /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 424
>          Bio::DB::Biblio::soap::get_all_ids('Bio::DB::Biblio:: soap=HASH(0xd800d8)') called at pubsearch.pl line 35
>Debugged program terminated.  Use q to quit or R to restart,
>   use O inhibit_exit to avoid stopping after program termination,
>   h q, h R or h O to get additional info.
>
>
>
>my $biblio = Bio::Biblio->new();
>     my $new_biblio=$biblio->find([$gene,$mod]);
>     my $results=$new_biblio->get_count;
>     if ($results) {
>       my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids};
>
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===============================
Baranidharan P
Senior Project Assistant
Bioinformatics Sub DIC
Dept of Biotechnology
Indian Institute of Technology
Kharagpur - 721302
West Bengal
INDIA
Ph.  +91 3222 281365