Hi all
Happy Christmas and Advanced wishes for a New year -2013
I have a doubt on table manipulation. pls help
Shown below is a table of entries, I want to have those gene records which contain SNP information. i. e the coordinates (start, end) of an SNP should lie within the regions of (start, end) of the gene. Ex: 1593 of SNP record is contained in (337, 2799) interval of the gene record. The output should just be the ID, locus_tag, gene_synonymn, db_xref.
How to do it. pls help
| referenceName | provenance | featureType | start | end | length | score | strand | phase | ID | locus_tag | gene_synonym | db_xref | featureSetName | locationType | referenceBase | alternativeBase | mutationType | variantQuality | depth | altFreqEM | numForwardRefAllele | numReverseRefAllele | numForwardAltAllele | numReverseAltAllele | mappingQuality | consensusQuality | genotypeGT | genotypePL | genotypeGQ | experimentName |
| NC_000913.2 | RefSeq | gene | 190 | 255 | 66 | . | 1 | . | NC_000913.2:thrL | b0001 | ECK0001 JW4367 | ECOCYC:EG11277 EcoGene:EG11277 GeneID:944742 | gene | |||||||||||||||||
| NC_000913.2 | RefSeq | gene | 337 | 2799 | 2463 | . | 1 | . | NC_000913.2:thrA | b0002 | ECK0002 Hs JW0001 thrA1 thrA2 thrD | ECOCYC:EG10998 EcoGene:EG10998 GeneID:945803 | gene | |||||||||||||||||
| NC_000913.2 | . | SNP | 1593 | 1593 | 1 | . | 1 | . | SNP Roche454 | EXACT | A | G | Transition | 96 | 9 | 1 | 0 | 0 | 3 | 6 | 20 | -54 | 1/1 | 129,27,0 | 51 | Roche454 | ||||
| NC_000913.2 | RefSeq | gene | 2801 | 3733 | 933 | . | 1 | . | NC_000913.2:thrB | b0003 | ECK0003 JW0002 | ECOCYC:EG10999 EcoGene:EG10999 GeneID:947498 | gene | |||||||||||||||||
| NC_000913.2 | RefSeq | gene | 3734 | 5020 | 1287 | . | 1 | . | NC_000913.2:thrC | b0004 | ECK0004 JW0003 | ECOCYC:EG11000 EcoGene:EG11000 GeneID:945198 | gene | |||||||||||||||||
| NC_000913.2 | RefSeq | gene | 5234 | 5530 | 297 | . | 1 | . | NC_000913.2:yaaX | b0005 | ECK0005 JW0004 | ECOCYC:G6081 EcoGene:EG14384 GeneID:944747 | gene |
