Module:Bio::DB::SeqFeature::Store

From BioPerl

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Pdoc documentation: Bio::DB::SeqFeature::Store	CPAN documentation: Bio::DB::SeqFeature::Store

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For details of how to use the module, see the associated perldoc.

See also

Bio::DB::SeqFeature 

The feature object customized to work well with DB::SeqFeature::Store

Bio::DB::SeqFeature::Store::GFF3Loader 

The GFF to Bio::DB::SeqFeature loader object

• Storage adaptors
  • Bio::DB::SeqFeature::Store::DBI::mysql
  • Bio::DB::SeqFeature::Store::berkeleydb
  • Bio::DB::SeqFeature::Store::memory

Notes

To get an overview of an existing DB::SeqFeature::Store database

The following code demonstrates how to get an overview of an existing DB::SeqFeature::Store database:

#!/usr/bin/perl -w
 
use strict;
use Bio::DB::SeqFeature::Store;
 
...
 
## $db is a DB::SeqFeature::Store object 
 
## Are sub-features being indexed?
print "Indexed sub-features? : ",
  $db->index_subfeatures, "\n";
 
## What serializer is being used?
print "The serializer is : ",
  $db->serializer, "\n";
 
## List all the feature types in the database:
print "Feature types:\n";
print join("\n", $db->types), "\n";
 
## List how many there are for each feature type in the database
print "Feature type counts:\n";
my %types = $db->types(-count => 1);
print join("\n", map { $_ . "\t". "$types{$_}" } keys %types), "\n";
 
## List the feature attributes (tags) in the database:
print "Attributes:\n";
print join("\n", $db->attributes), "\n";
 
## How many sequence ids in the database:
print "There are : ", scalar($db->seq_ids), " sequences in the database\n";
 
## How many features in the database:
print "There are : ", scalar($db->features), " features in the database\n";