[Bioperl-l] FASTA.pm issue

[lehvasla at ebi.ac.uk]

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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