[Bioperl-l] FASTA.pm issue

[Brian Osborne]

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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