[Bioperl-l] A problem with Bio::DB::Query::GenBank

liugai at 126.com liugai at 126.com
Thu Sep 14 08:06:25 UTC 2006

Hi Dear PPL
I am a fresh for bioperl. My problem happened when I am learning from HOWTO:Beginner-Bioperl. Would be there anyone kindly help me out? Thank you very much!
  a.. The version of Bioperl :1.5.1     
  b.. The platform or operating system : WinXp 
  c.. What you are trying to do:
To run following script in my machine:

#!/bin/perl -w
use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;

 $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
 $query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide',  -query => $query );

 $gb_obj = Bio::DB::GenBank->new;

 $stream_obj = $gb_obj->get_Stream_by_query($query_obj);

 while ($seq_obj = $stream_obj->next_seq) {
   # do something with the sequence object
   print $seq_obj->display_id, "\t", $seq_obj->length, "\n";

  a.. Any error messages. 

Can't locate IO/String.pm in @INC (@INC contains: D:\Perl\example\ D:/Perl/lib D
:/Perl/site/lib .) at D:/Perl/site/lib/Bio/DB/WebDBSeqI.pm line 83.
BEGIN failed--compilation aborted at D:/Perl/site/lib/Bio/DB/WebDBSeqI.pm line 8
Compilation failed in require at D:/Perl/site/lib/Bio/DB/NCBIHelper.pm line 80.
BEGIN failed--compilation aborted at D:/Perl/site/lib/Bio/DB/NCBIHelper.pm line
Compilation failed in require at D:/Perl/site/lib/Bio/DB/GenBank.pm line 123.
BEGIN failed--compilation aborted at D:/Perl/site/lib/Bio/DB/GenBank.pm line 123
Compilation failed in require at C:\DOCUME~1\wk\LOCALS~1\Temp\dir1D.tmp\query.pl
 line 3.
BEGIN failed--compilation aborted at C:\DOCUME~1\wk\LOCALS~1\Temp\dir1D.tmp\quer
y.pl line 3.

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