[Bioperl-l] trouble to retrieve sequence.. I'm a BEGINNER...

현도윤 dyhyun at rda.go.kr
Mon Dec 5 09:26:21 EST 2005


Hi,

I'm a bioperl beginner and studying bioperl code according to Beginners HOWTO.
I have a trouble in section 9. Retrievin a sequence from a database.
How can I solve this promblem? Please, help me~~

1. ver. of Bioperl : 1.4

2. OS : linux

3. I am trying to retrieve seq. from GenBank.

4. code
#!/usr/bin/perl -w

use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;

$query = "Arabidopsis[ORGN] AND topoisomerase[TITL] an 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";
}

5. error messages

Can't locate IO/String.pm in @INC (@INC contains: /usr/lib/perl5/5.6.0/i386-linux /usr/lib/perl5/5.6.0 /usr/lib/perl5/site_perl/5.6.0/i386-linux /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl .) at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm line 90.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm line 90.
Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm line 82.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm line 82.
Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/GenBank.pm line 124.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/GenBank.pm line 124.
Compilation failed in require at query.pl line 3.
BEGIN failed--compilation aborted at query.pl line 3.

ps. I read the FAQ pages. I found this answer. 
"NCBI changed the web CGI script that provided this access. You must be using bioperl <= 0.7.2. The developer release 0.9.3 contains this fix as does the 1.0 release." 
I cant't understand what it means....



More information about the Bioperl-l mailing list