User:Lindenb/Notebook/UMR915/20100927

=Moving SQL to mongo= VCFs

mysql -N -u anonymous \ -e 'select * from vcf_input' -D umr915 |\ awk -F ' ' '{printf("v={sqlid:%d,fileformat:\"%s\",filename:\"%s\",description:\"%s\",creation:\"%s\",projects:[\"XXX\"],individuals:[],headers:[]};db.vcfinputs.save(v);\n",$1,$2,$3,$4,$6);}' \ > jeter.js

indexes db.vcfinputs.ensureIndex({projects:1}) db.vcfinputs.ensureIndex({individuals:1}) add headers: mysql -u anonymous -N -e 'select distinct input_id,propValue from vcf_input_meta' -D umr915 |\ awk -F '  ' "{printf(\"v= db.vcfinputs.findOne({sqlid:%s}); if(v!=null) {v.headers.push(\'%s\');db.vcfinputs.save(v);}\n\",\$1,\$2);}"

> v=db.vcfinputs.findOne({sqlid:6}) { 	"_id" : ObjectId("4ca07bb0302820c9d33ff054"), "sqlid" : 6, "fileformat" : "PILEUP", "filename" : "XXXXX", "description" : "XXXXXX", "creation" : "2010-06-23 10:40:08", "projects" : [ "XX" ], 	"individuals" : [ ], "headers" : [ "##fileformat=VCFv3.3", "##filedate=2010-05-26 18:01:43", "##reference=NCBI36", "##dbSNP=dbSNP129", "##phasing=none", "##annotation=ensembl.54", "##INFO=DP,1,Integer,\"Total Depth\"", "##INFO=AC,1,String,\"Allele count\"", "##INFO=AN,1,Integer,\"Total number of alleles\"", "##INFO=MQ,1,Integer,\"MQ RMS mapping quality\"", "##INFO=CQ,1,String,Highest ensembl protein coding gene consequence\"", 		"##INFO=GN,1,String,\"Gene name\"", 		"##INFO=DB,1,Integer,\"dbSNP entry\"", 		"##INFO=HM3,0,Flag,\"Hapmap3 membership\"", 		"##INFO=PA,1,String,\"Population data\"", 		"##INFO=PS,1,String,\"Population source\"", 		"##INFO=NC,1,String,\"Nucleotide conservation (GERP)\"", 		"##INFO=CNV,0,Flag,\"In known CNV\"", 		"##INFO=MZ,1,Integer,\"Number of mapping quality zero reads\"" 	] }

Families
adding the 10 families in mongodb

stopping mongodb
stop mongodb mongo > use admin switched to db admin > db.shutdownServer