[Bioperl-l] FASTA.pm issue

[khoueiry]

Hi sumit,

I suggest you to change your index method. Try that... (In fact your
code and the below one works well for me)

------
#!/usr/bin/perl -w
use strict;
use Bio::Index::Fasta;


#Indexing....
my $type = $ENV{'BIOPER_INDEX_TYPE'};
if ($type) {
  $Bio::Index::Abstract::USE_DBM_TYPE = $type;
}

my $index = Bio::Index::Fasta->new( "/home/pierre/BioperlTest/f1.idx",
'WRITE' );
$index->make_index("/home/pierre/BioperlTest/f1");


my $seqobj = $index->fetch("abc");
my $str = $seqobj->seq();
print $str."\n";

exit; 

-----------

Le mercredi 06 juillet 2005 à 09:37 -0700, sumit middha a écrit :

> 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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