diff options
| -rw-r--r-- | SNPParser.sc | 200 |
1 files changed, 100 insertions, 100 deletions
diff --git a/SNPParser.sc b/SNPParser.sc index d3e89e9..6f33c63 100644 --- a/SNPParser.sc +++ b/SNPParser.sc @@ -1,107 +1,107 @@ SNPParser{ - var <placement; - var <comboDict; - var <file; - var <fileLength; - var <userID; - var <testSet; + var <placement; + var <comboDict; + var <file; + var <fileLength; + var <userID; + var <testSet; - *new{ - arg aFile, aTestSet = inf; - ^super.new.init(aFile, aTestSet); - } + *new{ + arg aFile, aTestSet = inf; + ^super.new.init(aFile, aTestSet); + } - init{ - arg aFile, aTestSet; - this.setFileAndUser(aFile); - testSet = aTestSet; - } + init{ + arg aFile, aTestSet; + this.setFileAndUser(aFile); + testSet = aTestSet; + } - setFileAndUser{//set the file (again) to be parsed - arg aFile; - var allSlash, allDot; - file = aFile; - allSlash = file.findAll("/"); - allDot = file.findAll("."); - if(allSlash.notNil,{//if there is no slash in the filename - userID = file[allSlash[allSlash.size-1]+1..allDot[allDot.size-2]-1].asInt; - },{ - userID = file[0..allDot[allDot.size-2]-1].asInt; - }); - userID.postln; - } + setFileAndUser{//set the file (again) to be parsed + arg aFile; + var allSlash, allDot; + file = aFile; + allSlash = file.findAll("/"); + allDot = file.findAll("."); + if(allSlash.notNil,{//if there is no slash in the filename + userID = file[allSlash[allSlash.size-1]+1..allDot[allDot.size-2]-1].asInt; + },{ + userID = file[0..allDot[allDot.size-2]-1].asInt; + }); + userID.postln; + } - readFile{//parse the file this parser currently is setup with - var found = false, company = ""; - "Guessing parser.".postln; - SNPInfo.sCompany.do({ - arg cCompany, i; - if(file.contains(cCompany.asString),{ - if(SNPInfo.workingSCompany.includes(i),{ - ("Attempting to parse a "++cCompany++" file now.").postln; - company = cCompany; - found = true; - },{ - ("Parsing files from "++cCompany++" is not supported (yet). Get me a coffee to make it work!").postln; - }); - }); - }); - if(found.not,{ - ("This file might not be supported at all: "++file).postln; - },{ - switch(company, - "23andme",{^this.parse23andme}, - {"No no no no no!".postln} - ); - }); - } + readFile{//parse the file this parser currently is setup with + var found = false, company = ""; + "Guessing parser.".postln; + SNPInfo.sCompany.do({ + arg cCompany, i; + if(file.contains(cCompany.asString),{ + if(SNPInfo.workingSCompany.includes(i),{ + ("Attempting to parse a "++cCompany++" file now.").postln; + company = cCompany; + found = true; + },{ + ("Parsing files from "++cCompany++" is not supported (yet). Get me a coffee to make it work!").postln; + }); + }); + }); + if(found.not,{ + ("This file might not be supported at all: "++file).postln; + },{ + switch(company, + "23andme",{^this.parse23andme}, + {"No no no no no!".postln} + ); + }); + } - parse23andme{//parsing a 23andme file: id, chromosome, position, base - var snpFile = File(file, "r"), line = "", counter = 0.0, tmp, snp, newSameCounter = 0.0; - fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace}); - ("File "++file++" is "++fileLength[0]++" lines long.").postln; - "Parsing might require some minutes! So kick back an get a coffee, while it lasts.".postln; - comboDict = SNPDict.new(fileLength[0], userID); - if(snpFile.isOpen,{ - protect{ - while{(line = snpFile.getLine).notNil}{//FIXME: Reinsert testset - if(line[0].asString!="#",{//skip commented lines - tmp = line.delimit({|ch| ch.isSpace});//delimit the line by space and/or tab - if(tmp[3].asString!="--" && (SNPInfo.isBasePair(tmp[3]) || SNPInfo.isBase(tmp[3]) && (SNPInfo.chromosomesLength[SNPInfo.convertChromosome(tmp[1])-1]>=tmp[2].asFloat)),{//skip empty SNPs and make sure it's either a single base or a base pair and ignore out-of-range SNPs (yes, science is unclear!) - if(SNPInfo.isBasePair(tmp[3]),{//if it's a base pair, set it up - snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], SNPInfo.createResolverForPair(tmp[3])); - },{ - if(SNPInfo.isBase(tmp[3]), {//if it's a single base, set it up - snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], \none); - }); - }); - newSameCounter = newSameCounter + comboDict.storeSNP(snp, SNPInfo.calcPosition(snp.chromosome, snp.position)); - switch(newSameCounter, - 1.0,{"Storing SNPs now: \n==========".postln;}, - 100000.0,{"=".post;}, - 200000.0,{"=".post;}, - 300000.0,{"=".post;}, - 400000.0,{"=".post;}, - 500000.0,{"=".post;}, - 600000.0,{"=".post;}, - 700000.0,{"=".post;}, - 800000.0,{"=".post;}, - 900000.0,{"=".post;}, - ); - }); - }); - counter = counter + 1; - }; - }{ - snpFile.close; - }; - },{ - ("Couldn't open file for reading: "++file).warn; - }); - "=".postln; - "Sorting lookup tables. This will also take some time!".postln; - comboDict.orderLookup(2); - "Done sorting lookup tables.".postln; - ^comboDict; - } + parse23andme{//parsing a 23andme file: id, chromosome, position, base + var snpFile = File(file, "r"), line = "", counter = 0.0, tmp, snp, newSameCounter = 0.0; + fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace}); + ("File "++file++" is "++fileLength[0]++" lines long.").postln; + "Parsing might require some minutes! So kick back an get a coffee, while it lasts.".postln; + comboDict = SNPDict.new(fileLength[0], userID); + if(snpFile.isOpen,{ + protect{ + while{(line = snpFile.getLine).notNil}{//FIXME: Reinsert testset + if(line[0].asString!="#",{//skip commented lines + tmp = line.delimit({|ch| ch.isSpace});//delimit the line by space and/or tab + if(tmp[3].asString!="--" && (SNPInfo.isBasePair(tmp[3]) || SNPInfo.isBase(tmp[3]) && (SNPInfo.chromosomesLength[SNPInfo.convertChromosome(tmp[1])-1]>=tmp[2].asFloat)),{//skip empty SNPs and make sure it's either a single base or a base pair and ignore out-of-range SNPs (yes, science is unclear!) + if(SNPInfo.isBasePair(tmp[3]),{//if it's a base pair, set it up + snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], SNPInfo.createResolverForPair(tmp[3])); + },{ + if(SNPInfo.isBase(tmp[3]), {//if it's a single base, set it up + snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], \none); + }); + }); + newSameCounter = newSameCounter + comboDict.storeSNP(snp, SNPInfo.calcPosition(snp.chromosome, snp.position)); + switch(newSameCounter, + 1.0,{"Storing SNPs now: \n==========".postln;}, + 100000.0,{"=".post;}, + 200000.0,{"=".post;}, + 300000.0,{"=".post;}, + 400000.0,{"=".post;}, + 500000.0,{"=".post;}, + 600000.0,{"=".post;}, + 700000.0,{"=".post;}, + 800000.0,{"=".post;}, + 900000.0,{"=".post;}, + ); + }); + }); + counter = counter + 1; + }; + }{ + snpFile.close; + }; + },{ + ("Couldn't open file for reading: "++file).warn; + }); + "=".postln; + "Sorting lookup tables. This will also take some time!".postln; + comboDict.orderLookup(2); + "Done sorting lookup tables.".postln; + ^comboDict; + } } |