[Bioperl-l] Question from HOWTO:Beginner-Bioperl

Brian Osborne osborne1 at optonline.net
Thu Sep 14 08:40:39 EDT 2006


liugai,

It looks like you need to install the module IO::String.

Brian O.


On 9/13/06 10:39 PM, "liugai at 126.com" <liugai at 126.com> wrote:

> Hi Dear
> 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?
>   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
> 3.
> 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
> 80.
> 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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