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jhannah@jaysnet-MacBook:~/src/bioperl-live/t/SeqFeature$ cat Store-SQLite.t | |
use Test::More tests => 2; | |
use strict; | |
use Bio::SeqIO; | |
use Bio::DB::SeqFeature::Store; | |
my $db = Bio::DB::SeqFeature::Store->new( | |
-adaptor => 'DBI::SQLite', | |
-dsn => 'test.sqlite', | |
-write => 1, | |
-create => 1, | |
); | |
my $in = Bio::SeqIO->new(-format=>'embl', -file=>"../data/test.embl"); | |
my $seq = $in->next_seq; | |
my $count; | |
foreach my $feat ($seq->get_SeqFeatures()) { | |
$db->store($feat); | |
last if (++$count == 3); | |
} | |
is($db->seq_ids, 1, "1 sequence loaded into test.sqlite"); | |
is($db->features, 3, "3 features loaded into test.sqlite"); | |
my $cmd = "perl ~/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS --adaptor=DBI::SQLite --dsn=test.sqlite"; | |
print "$cmd\n"; | |
# system ($cmd); | |
$ perl Store-SQLite.t | |
1..2 | |
ok 1 - 1 sequence loaded into test.sqlite | |
ok 2 - 3 features loaded into test.sqlite | |
$ perl ~/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS --adaptor=DBI::SQLite --dsn=test.sqlite | |
Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58. | |
jhannah@jaysnet-MacBook:~/src/bioperl-live/t/SeqFeature$ |
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