[Bioperl-l] FASTA.pm issue

[sumit middha]

Thanks for the reply Brian.
Changing it to Bio::Index::Fasta helped, but gave
another problem in my script, which I dont have a
clue.

------------- EXCEPTION  -------------
MSG: Can't open 'SDBM_File' dbm file
'../Dyak/dyak_chr_ucsc.fa.rev' : No such file or
directory
STACK Bio::Index::Abstract::open_dbm
/usr/local/lib/perl5/site_perl/5.8.5/Bio/Index/Abstract.pm:392
STACK Bio::Index::Abstract::new
/usr/local/lib/perl5/site_perl/5.8.5/Bio/Index/Abstract.pm:150
STACK Bio::Index::AbstractSeq::new
/usr/local/lib/perl5/site_perl/5.8.5/Bio/Index/AbstractSeq.pm:91
STACK toplevel get_ortho.pl:31

I know that the file exists, and has been formatted as
a database to use BLAST search.

sumit

--- Brian Osborne <brian_osborne at cognia.com> wrote:

> Sumit,
> 
> In perl 5.8 a module that's using a tied hash is
> supposed to have an EXISTS
> method, but it appears that AnyDBM_File doesn't. You
> could try using
> Bio::Index::Fasta instead, or Bio::DB::Flat.
> 
> Brian O.
> 
> 
> On 6/22/05 6:24 PM, "sumit middha"
> <sm_middha at yahoo.com> wrote:
> 
> > 
> > Hello,
> > 
> > I have a trouble with using fasta module
> > 
> > I use the required statements
> > 
> > use Bio::DB::Fasta;
> > use Bio::Seq;
> > 
> > The error was:
> > 
> > AnyDBM_File doesn't define an EXISTS method at
> >
> /usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/Fasta.pm
> > line 577
> > 
> > thanks,
> > sm
> > 
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