User:Lindenb/Notebook/UMR915/20100929

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.png

20100928        Top        20100930       


Generating individuals for biomonogo

from the file I wrote yesterday:

  cat jeter.ped  | grep r | sort  | sort | sed 's/Br//' |\
  awk -F '   ' '{printf("i={_id:\"Brs%s.%s\",name:\"%s\",sex:%s,familyId:{$ref:\"families\",$id:\"Br%s\"},labels:[],dead:false,fatherId:",$1,$2,$2,$5,$1); if($3=="0") {printf("null");} else { printf("{$ref:\"individuals\",$id:\"Brs%s.%s\"}",$1,$3);} printf(",motherId:");  if($4=="0") {printf("null");} else { printf("{$ref:\"individuals\",$id:\"Brs%s.%s\"}",$1,$4);} printf("};  db.individuals.save(i);\n"); }'

generating mongo scripts from mysql

updated my stylesheet: http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/sql2json.xsl to support Mongodb

  xsltproc --stringparam mongo bams ~/src/lindenb/src/xsl/sql2json.xsl  ~/jeter.xml 
  record={_id:1,"filename":"/GENOTYPAGE/data/xxxx.bam","sample_id":1,"description":"Fastq","meta":"{}","creation":"2010-06-30 17:25:24","modified":"2010-06-30 17:25:24"};
  db.bams.save(record);

Updated table vcfinputs

 function castindi(id)
         {
         switch(id)
                 {
                 case 3: case 4: case 27: case 45: case 57: return "XXXXX1.6";
                 case 5: case 6: case 28: case 46: case 58: return "XXXXX2.3";
                 case 7: case 8: case 29: case 47: case 59: return "XXXXX3.11";
                 case 9: case 10: case 30: case 48: case 60: return "XXXXX4.12";
                 case 11: case 12: case 31: case 49: case 61: return "XXXXX5.12";
                 case 13: case 14: case 32: case 50: case 62: return "XXXXX6.30";
                 case 15: case 16: case 33: case 51: case 63: return "XXXXX7.3";
                 case 17: case 18: case 34: case 52: case 64:  return "XXXXX8.11";
                 case 19: case 20: case 35: case 53: case 65: return "XXXXX9.11";
                 case 21: case 22: case 36: case 54: case 66:return "XXXXX10.10";
                 }
         return null;
         }
 
 var c= db.vcfinputs.find();
 while(c.hasNext())
         {
         var rec= c.next();
         var indi= castindi(rec.sqlid);
         if(indi==null) continue;
         delete rec.individuals;
         rec.individualIds=[indi];
         db.vcfinputs.save(rec);
         }