[Bioperl-l] FASTA.pm issue
brian_osborne at cognia.com
Thu Jun 23 14:38:06 EDT 2005
You'll have to show us the code that gives you the error, I think.
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
> ------------- EXCEPTION -------------
> MSG: Can't open 'SDBM_File' dbm file
> '../Dyak/dyak_chr_ucsc.fa.rev' : No such file or
> STACK Bio::Index::Abstract::open_dbm
> STACK Bio::Index::Abstract::new
> STACK Bio::Index::AbstractSeq::new
> STACK toplevel get_ortho.pl:31
> I know that the file exists, and has been formatted as
> a database to use BLAST search.
> --- Brian Osborne <brian_osborne at cognia.com> wrote:
>> 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:
>>> 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
>>> line 577
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