[Bioperl-l] FASTA.pm issue

[sumit middha]

Well heres a small test code I made to explain my
problem. Please let me know your suggestions.
Thanks.

--------------code-----------------
#!/usr/bin/perl -w
use strict;
use Bio::DB::Fasta;
use Bio::DB::Flat;
use Bio::Index::Fasta;
use Bio::Seq;

my $db = Bio::DB::Fasta->new("f1");
#my $db = Bio::Index::Fasta->new("f1");
my $seqobj = $db->get_Seq_by_id("abc"); 
my $str = $seqobj->seq();
print $str;

exit; 
-----------end of code ------------

And here is the error I get (which I did not a few
months back)

> perl -w test.pl
AnyDBM_File doesn't define an EXISTS method at
/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/Fasta.pm
line 577

and f1 fasta file is 
> cat f1
>abc
AGCATCG


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

> Sumit,
> 
> You'll have to show us the code that gives you the
> error, I think.
> 
> 
> Brian O.
> 
> 
> On 6/23/05 1:07 PM, "sumit middha"
> <sm_middha at yahoo.com> wrote:
> 
> > 
> > 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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