[Bioperl-l] indexing and accessing local database

[Qunfeng Dong]

Brian, Thanks for the suggestion, I didn't use Bio::DB::Fasta because I couldn't
find any Doc about how to reuse the index instead of generating it every time.
Anyway, I tried the following code
****************************************
#!/usr/bin/perl -w
#name: DBindex.pl
use Bio::DB::Fasta;
$File_Name = shift;
$inx = Bio::DB::Fasta->new($File_Name);
$seq = $inx->get_Seq_by_id("AF468672");
print $seq->seq;
*****************************************
then ran it as
% DBindex.pl fastaFile
then I got the following error msg 

Use of uninitialized value in numeric lt (<) at
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Fasta.pm line 604.
Odd number of elements in hash assignment at
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Fasta.pm line 969.
Use of uninitialized value in numeric gt (>) at
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Fasta.pm line 817.



Something must be wrong. Maybe I shouldn't use BioPerl and stick to the blast
database with fastacmd :-)


Qunfeng


> Qunfeng,
> 
> I'm also seeing a segmentation fault on my Cygwin/Windows machine with code
> like yours, using Bio::Index::Fasta. But I'm surprised that I can index
> using Bio::DB::Fasta. If you don't care which indexing module you're using
> then I suggest you try something like this and see what happens:
> 
> use Bio::DB::Fasta;
> $File_Name = shift;
> $inx = Bio::DB::Fasta->new($File_Name);
> $seq = $inx->get_Seq_by_id("P8413");
> print $seq->seq;
> 
> 
> Brian O.
> 
> -----Original Message-----
> From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Qunfeng Dong
> Sent: Tuesday, July 09, 2002 12:44 PM
> To: Jason Stajich
> Cc: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] indexing and accessing local database
> 
> It's Linux and perl 5 (and when I install bioperl, perl is also installed)
> 
> 
> > What operating system are you using and version of Perl?
> >
> > On Tue, 9 Jul 2002, Qunfeng Dong wrote:
> >
> > > Hi,
> > >
> > > I am trying to follow the sample code from
> > >
> http://bioperl.org/Core/POD/bptutorial.html#III_1_1_Accessing_remote_databas
> > >
> > > to build a local fasta sequence database
> > >  #!/usr/bin/perl -w
> > >  #scriptName - BuildIndex.pl
> > >   use Bio::Index::Fasta; # using fasta file format
> > >   $Index_File_Name = shift;
> > >   $inx = Bio::Index::Fasta->new(
> > >       -filename => $Index_File_Name,
> > >       -write_flag => 1);
> > >   $inx->make_index(@ARGV);
> > >
> > >
> > > then I ran the script BuildIndex.pl as
> > > % BuildIndex.pl indexName FastaSeqName
> > > and I got Segmentation fault. Any idea why?
> > >
> > > Qunfeng Dong
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> >
> 
> 
> Qunfeng Dong, Ph.D
> ZmDB Manager
> 2104 Molecular Biology Building
> Iowa State University
> Ames, IA 50010
> 
> 
> 
> 
> 
> 
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Qunfeng Dong, Ph.D
ZmDB Manager 
2104 Molecular Biology Building
Iowa State University
Ames, IA 50010