[Bioperl-l] FileCache.pm error

[Jason Stajich]

Did you make the directory
/tmp/cache
on your machine?

The FileCache stuff is overkill depending on what you want to.

You can also leave it out by just saying:

my $cachent = $ntdb;
my $cachepep= $pepdb;

-jason
On Sun, 20 Jun 2004, Marcelino Suzuki wrote:

> 	I am trying to run a script for getting CDS out of Genbank by Jason
> Stajich below that I saved as test2.pl, and get the following error
> message, that I believe is caused by my bioperl configuration (I just
> installed bioperl in MacOS X:
>
> 	------------- EXCEPTION  -------------
> MSG: Could not open primary index file
> STACK Bio::DB::FileCache::_open_database
> /Library/Perl/5.8.1/Bio/DB/FileCache.pm:321
> STACK Bio::DB::FileCache::new
> /Library/Perl/5.8.1/Bio/DB/FileCache.pm:127
> STACK toplevel test2.pl:14
>
> 	Does anyone have any idea why I get this error?
>
> 	Thanks
>
> 	Marcelino
>
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::DB::GenBank;
> use Bio::DB::GenPept;
> use Bio::DB::FileCache;
> use Bio::Factory::FTLocationFactory;
> use Bio::SeqFeature::Generic;
>
> my $ntdb = new Bio::DB::GenBank;
> my $pepdb= new Bio::DB::GenPept;
>
> # do some caching in the event you're pulling up the same
> # chromosome and/or you are debugging
> my $cachent = new Bio::DB::FileCache(-kept => 1,
>                                       -file => '/tmp/cache/nt.idx',
>                                       -seqdb => $ntdb);
>
> my $cachepep = new Bio::DB::FileCache(-kept => 1,
>                                        -file => '/tmp/cache/pep.idx',
>                                        -seqdb => $pepdb);
>
> # obj to turn strings into Bio::Location object
> my $locfactory = new Bio::Factory::FTLocationFactory;
>
> # you might get these from a file (and they can be accessions too)
> my @protgis = (10956263);
>
> foreach my $gi ( @protgis ) {
>    my $protseq = $cachepep->get_Seq_by_id($gi);
>    if( ! $protseq ) { print STDERR "could not find a seq for gi:$gi\n";
>                       next;
>                     }
>    foreach my $cds (  grep { $_->primary_tag eq 'CDS' }
>                            $protseq->get_SeqFeatures() )
>    {
>       next unless( $cds->has_tag('coded_by') ); # skip CDSes with no
> coded_by
>       my ($codedby) = $cds->each_tag_value('coded_by');
>       my ($ntacc,$loc) = split(/\:/, $codedby);
>       $ntacc =~ s/(\.\d+)//; # genbank wants an accession not a
> versioned one
>       my $cdslocation = $locfactory->from_string($loc);
>       my $cdsfeature = new Bio::SeqFeature::Generic(-location =>
> $cdslocation);
>       my $ntseq = $cachent->get_Seq_by_acc($ntacc);
>       next unless $ntseq;
>       $ntseq->add_SeqFeature($cdsfeature); # locate the feature on a seq
>       my $cdsseq = $cdsfeature->spliced_seq();
>       print "cds seq is ", $cdsseq->seq(), "\n";
>   }
> }
>
>
>
> ========================================================================
> ====
>              oOOOOo           			Marcelino Suzuki,  Assistant Professor
>            oOOO            Chesapeake Biological Lab - Univ of Maryland
> Center Environm Science
>         oOOOOOo.          		PO Box 38, One Williams St Solomons, MD 20688
>      .oOOOOOOOOOo.                      suzuki at cbl.umces.edu  -
> http://cbl.umces.edu
>    .oOOOOOOOOOOOOOOooo..    	 Ph 410-326-7291   FAX 410-326-7341
> 000000000000000000000000000000000000000000000000000000000000000000000000
> 0000
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu