-- This script parses the table of genes from http://geneticassociationdb.nih.gov/ -- and generates an annotated interval list for use with the GATK -- -- Author: carneiro -- Date: 5/24/2011 ref_table = { "ID", "AS", "PH", "DI", "DC", "DT", "CH", "CB", "GE", "ST", "SP", "PV", "RE", "PI", "AA", "AF", "PC", "GN", "RS", "PO", "GO", "SU", "LN", "UN", "NP", "MP", "JO", "TI", "RN", "OM", "YR", "CN", "SI", "EF", "GIGA", "GIAA", "GIGB", "GIAB", "GIGC", "GIAC", "GIAS", "GIEF" } chr_limits = { 249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569 } local header = [[@HD VN:1.0 SO:coordinate @SQ SN:1 LN:249250621 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens @SQ SN:2 LN:243199373 AS:GRCh37 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M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus]] local function comp(a, b) if a.chr == b.chr then return a.start < b.start end local x = tonumber(a.chr) local y = tonumber(b.chr) if x and y then return x < y end return a.chr < b.chr end local function cleanNumber (x) local t = x:gsub(",","") return tonumber(t) end local function cleanDisease (x) local d = x:gsub("[^%w%s]", "") return d:gsub(" ", "_") end local function isSameGene (g1, g2) return g1.chr == g2.chr and g1.start == g2.start and g1.finish == g2.finish end local function isValidGene(gene) local x if gene.chr == "X" then x = 23 elseif gene.chr == "Y" then x = 24 elseif gene.chr == "MT" then x = 25 else x = tonumber(gene.chr) end return x >= 1 and x <= 25 and gene.start < gene.finish and chr_limits[x] > gene.finish end local function addGene(geneTable, gene) if isValidGene(gene) then -- only adds valid genes local geneAdded = false for _, g in ipairs(geneTable) do if isSameGene(gene, g) then geneAdded = true if g.disease ~= gene.disease then g.disease = g.disease .. ","..gene.disease end end end if (not geneAdded) then table.insert(geneTable, gene) end end end local function cleanIntervals(f, t) for l in io.lines(f) do local counter = 1 local id, c, b, e, disease for match in l:gmatch("(.-);;") do -- print("DEBUG: ", counter, match) if counter == 1 then id = match elseif counter == 3 then disease = cleanDisease(match) elseif counter == 7 then c = match elseif counter == 10 then b = cleanNumber(match) elseif counter == 11 then e = cleanNumber(match) end counter = counter + 1 end if id and c and b and e and c~= "" then addGene(t, {id=id, chr=c, start=b, finish=e, disease=disease}) end end return table.sort(t, comp) end local function printIntervals(t) print(header) for _,interval in ipairs(t) do print(interval.chr,interval.start,interval.finish, "+", interval.id..":::"..interval.disease) end end t = {} cleanIntervals(arg[1], t) printIntervals(t) --[[ -- REFERENCE TABLE 1 ID 2 Association(Y/N) 3 Broad Phenotype 4 Disease Class 5 Disease Class Code 6 MeSH Disease Terms 7 Chromosom 8 Chr-Band 9 Gene 10 DNA Start 11 DNA End 12 P Value 13 Reference 14 Pubmed ID 15 Allele Author Description 16 Allele Functional Effects 17 Polymophism Class 18 Gene Name 19 RefSeq 20 Population 21 MeSH Geolocation 22 Submitter 23 Locus Number 24 Unigene 25 Narrow Phenotype 26 Mole. Phenotype 27 Journal 28 Title 29 rs Number 30 OMIM ID 31 Year 32 Conclusion 33 Study Info 34 Env. Factor 35 GI Gene A 36 GI Allele of Gene A 37 GI Gene B 38 GI Allele of Gene B 39 GI Gene C 40 GI Allele of Gene C 41 GI Association? 42 GI combine Env. Factor --]]