new genome_statistics table

generated test data for patch test database
database patched up to release 75

modules/t/genomeContainer.t

@@ -85,7 +85,7 @@ is($alt_lnoncoding_count, $genome->get_alt_lnoncoding_count, "Long non coding co
 my $alt_snoncoding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['snoncoding_acnt']);
 is($alt_snoncoding_count, $genome->get_alt_snoncoding_count, "Short non coding count on alternate sequences is correct");
 
-my $short_variation_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['SNPcount'], -NO_ERROR => 1);
+my $short_variation_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['SNPCount'], -NO_ERROR => 1);
 is($short_variation_count, $genome->get_short_variation_count, "Short variants count is correct");
 
 is_rows($genome->get_prediction_count, $db, "prediction_transcript");
@@ -108,6 +108,7 @@ is($ref_length, $genome->get_ref_length, "Reference length is correct");
 
 $sql = "SELECT sum(length(sequence)) FROM dna";
 my $total_length = $sql_helper->execute_single_result(-SQL => $sql);    
+print "$total_length is the calculated sql length\n";
 is($total_length, $genome->get_total_length, "Total length is correct");
 
 

modules/t/test-genome-DBs/homo_sapiens/patch/attrib_type.txt

@@ -251,3 +251,6 @@
 389	snoncoding_cnt	Short non coding gene count	Number of short non coding genes
 390	lnoncoding_cnt	Long non coding gene count	Number of long non coding genes
 391	TlUPsCount	translated_unprocessed_pseudogene	Number of Translated Unprocessed Pseudogenes
+392	genscan	Genscan transcripts	Transcripts predicted using Genscan
+393	ref_length		\N
+394	total_length		\N

modules/t/test-genome-DBs/homo_sapiens/patch/genome_statistics.txt

+26	lnoncoding_acnt	4	1	388	2013-11-28 09:42:06
+32	snoncoding_cnt	1	1	389	2013-11-28 09:42:06
+36	SNPCount	5724063	1	10	2013-11-28 09:52:41
+33	total_length	967294	1	394	2013-11-28 09:42:06
+31	pseudogene_cnt	1	1	67	2013-11-28 09:42:06
+29	snoncoding_acnt	1	1	387	2013-11-28 09:42:06
+30	ref_length	326385627	1	393	2013-11-28 09:42:06
+28	lnoncoding_cnt	5	1	390	2013-11-28 09:42:06
+27	coding_cnt	7	1	64	2013-11-28 09:42:06
+25	pseudogene_acnt	0	1	370	2013-11-28 09:42:06
+35	PredictionTranscript	18	1	392	2013-11-28 09:42:09
+34	coding_acnt	4	1	369	2013-11-28 09:42:06

modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt

-1	\N	schema_version	74
+1	\N	schema_version	75
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -48,3 +48,8 @@
 2054	\N	patch	patch_73_74_d.sql|remove_qtl
 2055	\N	patch	patch_73_74_e.sql|remove_canonical_annotation
 2056	\N	patch	patch_73_74_f.sql|remove_pair_dna_align
+2057	\N	patch	patch_73_74_g.sql|add_transcript_idx_tise
+2058	\N	patch	patch_73_74_h.sql|add_genome
+2059	\N	patch	patch_74_75_a.sql|schema_version
+2060	\N	patch	patch_74_75_b.sql|transcript_source
+2061	\N	patch	patch_74_75_c.sql|add_genome_statistics

modules/t/test-genome-DBs/homo_sapiens/patch/table.sql

@@ -103,7 +103,7 @@ CREATE TABLE `attrib_type` (
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=394 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=395 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -320,6 +320,29 @@ CREATE TABLE `gene_attrib` (
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
+CREATE TABLE `genome` (
+  `stats_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `statistics` varchar(128) NOT NULL,
+  `value` int(10) unsigned NOT NULL DEFAULT '0',
+  `species_id` int(10) unsigned DEFAULT '1',
+  `attribute` varchar(128) DEFAULT NULL,
+  `timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+  PRIMARY KEY (`stats_id`),
+  KEY `stats_idx` (`statistics`,`attribute`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `genome_statistics` (
+  `genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `statistic` varchar(128) NOT NULL,
+  `value` int(10) unsigned NOT NULL DEFAULT '0',
+  `species_id` int(10) unsigned DEFAULT '1',
+  `attrib_type_id` int(10) unsigned DEFAULT NULL,
+  `timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+  PRIMARY KEY (`genome_statistics_id`),
+  UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
+  KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `identity_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
   `xref_identity` int(5) DEFAULT NULL,
@@ -449,7 +472,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2057 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2062 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -747,6 +770,7 @@ CREATE TABLE `transcript` (
   `seq_region_end` int(10) unsigned NOT NULL,
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
+  `source` varchar(20) NOT NULL,
   `biotype` varchar(40) NOT NULL,
   `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
   `description` text,
@@ -778,7 +802,8 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
   `intron_supporting_evidence_id` int(10) unsigned NOT NULL,
   `previous_exon_id` int(10) unsigned NOT NULL,
   `next_exon_id` int(10) unsigned NOT NULL,
-  PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
+  PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`),
+  KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_supporting_feature` (