[Bioperl-l] Bio::DB::Fasta problem

Scott Cain scott at scottcain.net
Tue Dec 7 15:08:56 EST 2010


Hi Maxim,

I think you have a scope problem.  If you declare the variable $db
inside of the if block, it ceases to exist when exiting the block.
Put the "my $db;" before the if block so that it will continue to
exist.

Scott


On Tue, Dec 7, 2010 at 3:00 PM, Maxim <deeepersound at googlemail.com> wrote:
> Hi,
>
> I'm using Bio::DB::Fasta to retrieve sequences. This works like a charm
> (super fast!!!), for example like in the script below, where bed-files are
> taken as input.
>
> My problem: as soon as the initialization of the fasta directory index is
> called from within an if-statement, I get an error like:
>
> Can't call method "get_Seq_by_id" on an undefined value at
> extract_bed_bio_db_fasta_test.pl line 20, <INP> line 134.
>
>
> The script is as simple as this, the error comes up when I use the full
> script (including the 2 out-commented lines):
>
> use Bio::Perl;
> use Bio::DB::Fasta;
>
> $bedFileName=@ARGV[0];
> $genome = @ARGV[1];
> #if ($genome eq "mm9") {
> my $db      = Bio::DB::Fasta->new('/Users/Computing/BIODBFASTA/mm9_masked');
> #}
>
> open (INP, "$bedFileName");
> foreach (<INP>)
> {
> @words = split /\s+/, $_; ### 0-chr 1-start 2-end
> $chr = @words[0];$chr =~s/\s+//g;
> $start = @words[1];$start =~s/\s+//g;
> $end = @words[2];$end =~s/\s+//g;
>   $fast_name = $chr . "_" . $start . "_" . $end;
> my $obj     = $db->get_Seq_by_id($chr);
> $subseq  = $obj->subseq($start => $end);
> print ">", "$fast_name\n";
> print "$subseq\n";
> }
>
> What is the problem when initializing from within the if-statement?
>
> I really appreciate all kind of advice, I guess the reason is rather simple,
> but I do not get it.
> Regards
> Maxim
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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