使用MySQL製做SNP146數據庫

SNP數據（txt）文件能夠在此下載：http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

下載、解壓data以後，啓動MySQL server，登陸進入MySQL

# create database
create database snp146all
use snp146all

# create table:這一步的MySQL script文件能夠在上面提到的網站下載 
DROP TABLE IF EXISTS `snp146`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `snp146` (
  `bin` smallint(5) unsigned NOT NULL,
  `chrom` varchar(31) NOT NULL,
  `chromStart` int(10) unsigned NOT NULL,
  `chromEnd` int(10) unsigned NOT NULL,
  `name` varchar(15) NOT NULL,
  `score` smallint(5) unsigned NOT NULL,
  `strand` enum('+','-') NOT NULL,
  `refNCBI` blob NOT NULL,
  `refUCSC` blob NOT NULL,
  `observed` varchar(255) NOT NULL,
  `molType` enum('unknown','genomic','cDNA') NOT NULL,
  `class` enum('unknown','single','in-del','microsatellite','named','mnp','insertion','deletion') NOT NULL,
  `valid` set('unknown','by-cluster','by-frequency','by-submitter','by-2hit-2allele','by-hapmap','by-1000genomes') NOT NULL,
  `avHet` float NOT NULL,
  `avHetSE` float NOT NULL,
  `func` set('unknown','coding-synon','intron','near-gene-3','near-gene-5','ncRNA','nonsense','missense','stop-loss','frameshift','cds-indel','untranslated-3','untranslated-5','splice-3','splice-5') NOT NULL,
  `locType` enum('range','exact','between','rangeInsertion','rangeSubstitution','rangeDeletion','fuzzy') NOT NULL,
  `weight` int(10) unsigned NOT NULL,
  `exceptions` set('RefAlleleMismatch','RefAlleleRevComp','DuplicateObserved','MixedObserved','FlankMismatchGenomeLonger','FlankMismatchGenomeEqual','FlankMismatchGenomeShorter','SingleClassLongerSpan','SingleClassZeroSpan','SingleClassTriAllelic','SingleClassQuadAllelic','ObservedWrongFormat','ObservedTooLong','ObservedContainsIupac','ObservedMismatch','MultipleAlignments','NonIntegerChromCount','AlleleFreqSumNot1','SingleAlleleFreq','InconsistentAlleles') NOT NULL,
  `submitterCount` smallint(5) unsigned NOT NULL,
  `submitters` longblob NOT NULL,
  `alleleFreqCount` smallint(5) unsigned NOT NULL,
  `alleles` longblob NOT NULL,
  `alleleNs` longblob NOT NULL,
  `alleleFreqs` longblob NOT NULL,
  `bitfields` set('clinically-assoc','maf-5-some-pop','maf-5-all-pops','has-omim-omia','microattr-tpa','submitted-by-lsdb','genotype-conflict','rs-cluster-nonoverlapping-alleles','observed-mismatch') NOT NULL,
  KEY `name` (`name`),
  KEY `chrom` (`chrom`,`bin`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

# load data
load data infile 'snp146.txt' into table snps fields terminated by '\t' lines terminated by '\n';

這樣就製做完成！

然而，另外一個問題天然而然地顯現：SNP146 database大約佔用20+GB的硬盤，因此，須要將其MySQL的存儲用的database從default的地方移動到空間更多的地方。這個問題等待下文解決。