[Bioperl-l] FASTA.pm issue

[sumit middha]

Mine is 

> perl -v

This is perl, v5.8.5 built for sun4-solaris

> perl -MAnyDBM_File -le 'print AnyDBM_File->VERSION;'
1.00

:( any guesses ??


--- lehvasla at ebi.ac.uk wrote:

> 
> Dumit,
> 
> Your code works under perl v5.8.4. I do not get any
> errors or warnings.
> There has to be some change between perl releases.
> What is the version of
> your AnyDBM_File? Mine is
> 
> perl -MAnyDBM_File -le 'print AnyDBM_File->VERSION;'
> 1.00
> 
>      -Heikki
> 
> 
> >
> > 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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> 
> 
> 



		
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