my attempt at SeqFeature.t

gistfile1.pl

# -*-Perl-*- Test Harness script for Bioperl
# $Id$


## I'm confused about the tests here, so for the sake of simplicity
## I'm going to start from scratch. Basically I just want to write a
## few tests to show up some specific bugs. Of course the right thing
## to do is to create another test file, but I don't know how to get
## SeqFeature_mysql.t to point at it (that file is automatically
## generated at build time).


use strict;
use warnings;

use constant TEST_COUNT => 10;

BEGIN {
  
  #use Data::Dumper;
  
  ## What does this do then?
  use Bio::Root::Test;
  
  ## Set up the test plan
  test_begin(-tests => TEST_COUNT);
  
  use_ok('Bio::DB::SeqFeature::Store');
  use_ok('Bio::DB::SeqFeature::Store::GFF3Loader');

  #    use_ok('Bio::Root::IO');
#    use_ok('Bio::DB::Fasta');
#    use_ok('File::Copy');
}



## What is this then?
my $DEBUG = test_debug();

## This is how different adaptors are tested, by calling the test
## script, for example, with different values for --dsn (see below).
my @args = @ARGV;



## Set up our tests...

my $gff_file =
  test_input_file('gene_test.gff');

my $TMP = File::Spec->tmpdir();




## Create a Bio::DB::SeqFeature::Store connection object using the
## values passed by the user at build time (see 'SeqFeature_mysql.t',
## 'SeqFeature_BDB.t', etc.)

## Note, extra 'args' are added to the new call here to mirror
## bp_seqfeature_load.pl as far as possible.

## NB: -adaptor -create -dsn -user and -password are all supplied in
## in 'SeqFeature_mysql.t'.

my $db = Bio::DB::SeqFeature::Store->
  new( @args,
       -namespace => undef,
       -tmpdir => $TMP,
       -write => 1,
       -compress => 0,
     );

ok($db);


## Again, copying bp_seqfeature_load.pl to get this bug to show up...
ok( $db->init_database('erase') );


## Create a loader to load our GFF file

my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->
  new( -store=> $db,
       -sf_class => 'Bio::DB::SeqFeature',
       -verbose => 1,
       -tmpdir  => $TMP,
       -fast => 0,
       -ignore_seqregion => 0,
       -index_subfeatures  => 1,
       -noalias_target => 0,
       -summary_stats => 1,
     );

ok($loader);



## Try to pin down the weird "Use of uninitialized value in length at
## /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
## line 1064." bug...


## Load the GFF
ok($loader->load($gff_file));

## Query some features
my @features =
  $db->features( -seq_id => 'chr10',
		 -start  => 1,
		 -end    => 1700000,
		 -type   => 'gene',
	       );

## How many sequence ids in the database?
warn 'There are : '. scalar $db->seq_ids.
  " sequences in the database\n";



warn "\t\tgot ", scalar @features, " features \n";




__END__