diff options
Diffstat (limited to 'SNPFile.sc')
| -rw-r--r-- | SNPFile.sc | 167 |
1 files changed, 167 insertions, 0 deletions
diff --git a/SNPFile.sc b/SNPFile.sc new file mode 100644 index 0000000..a811d6f --- /dev/null +++ b/SNPFile.sc @@ -0,0 +1,167 @@ +SNPFile{ + var <snpDict; + var <file; + var <fileLength; + var <userID; + var <testSet = inf; + *new{ + arg aFile, aTestSet = inf; + ^super.new.init(aFile, 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; + }); + } + + readFile{//read a SNPDict from file + var snpFile = File(file, "r"), line = "", counter = 0, procCounter = Array.new(9), tmp, key, sizeOf, snp, res, keyCount = 0.0, unknown, unknownCount = 0.0; + fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace}); + 9.do({|item,i| procCounter.add(round((fileLength[0].asFloat/100)*(i+1)*10, 1).asInt)});//calculating procentuals for a simple progression output + ("Now reading: "++file++" ("++fileLength[0]++" lines).").postln; + ("==========").postln; + if(snpFile.isOpen,{ + protect{ + while{(line = snpFile.getLine).notNil }{ + switch(line[0].asString, + "*",{//info line + sizeOf = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab + snpDict = SNPDict.new(sizeOf[1].asFloat, sizeOf[3].asInt);//init new SNPDict + snpDict.initLookupFromFile(sizeOf[1].asFloat, sizeOf[2].asFloat); + }, + ";",{//key line + key = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab + snpDict.addPositionLookupFromFile(keyCount, key[1].asFloat);//store to lookup table! + keyCount = keyCount + 1.0; + }, + "+",{//SNP line + tmp = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab + if(tmp[6].isNil,{ + res = [tmp[5].asSymbol]; + },{ + res = [tmp[5].asSymbol, tmp[6].asSymbol]; + }); + snp = SNP.new(tmp[1], tmp[2], tmp[3], tmp[4], res); + snpDict.storeSNP(snp, key[1]); + }, + "|",{//unknown line + unknown = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab + snpDict.addUnknownLookupFromFile(unknownCount, unknown[1].asFloat); + unknownCount = unknownCount + 1.0; + } + ); + counter = counter + 1; + switch(counter, + procCounter[0],{"=".post;}, + procCounter[1],{"=".post;}, + procCounter[2],{"=".post;}, + procCounter[3],{"=".post;}, + procCounter[4],{"=".post;}, + procCounter[5],{"=".post;}, + procCounter[6],{"=".post;}, + procCounter[7],{"=".post;}, + procCounter[8],{"=".post;} + ); + }; + "=".postln; + "Done reading file to RAM.".postln; + }{ + snpFile.close; + }; + },{ + ("Couldn't open file for reading: "++file).warn; + }); + ^snpDict; + } + + writeFile{//write a SNPDict to file + arg snpDict; + var snpFile = File(file, "w"), line = "", counter = 0, tmp, snp, newSameCounter = 0; + ("Attempting to write SNPDict to file: "++file).postln; + if(snpFile.isOpen, { + protect{ + snpFile.write("*\t"++snpDict.snpArr.size.asString++"\t"++snpDict.unknownArr.size.asString++"\t"++snpDict.userID++"\n");//write length of snpArr and unknownArr + snpDict.snpArr.do({ + arg item; + snpFile.write(";\t"++item.asString++"\n"); + snpDict.snpAtPosition(item).do({//write all SNPs + arg snp; + var res; + if(snp.resolver.size==2,{ + res = (snp.resolver[0]++"\t"++snp.resolver[1]).asString; + },{ + res = snp.resolver[0].asString; + }); + snpFile.write("+\t"++snp.chromosome.asString++"\t"++snp.position.asString++"\t"++snp.id.asString++"\t"++snp.base.asString++"\t"++res++"\n");//write SNP to file + }); + }); + snpDict.unknownArr.do({//write all unknown positions + arg item; + snpFile.write("|\t"++item.asString++"\n"); + }); + }{ + snpFile.close; + ("Done writing to file.").postln; + ^true; + }; + },{ + ("Couldn't open file for writing: "++file).postln; + ^false; + }); + } + + writeUnknownIDToFile{//write the rsids of all unknown SNPs to file + arg snpDict; + var snpFile = File("/media/Data/tmp/1/1.unknown.snp", "w"); + ("Attempting to write unknowns to file: "++file).postln; + if(snpFile.isOpen, { + protect{ + snpDict.unknownArr.do({ + arg item,i; + snpDict.noneResolverAtPosition(item).do({ + arg snp,i; + snpFile.write(snp.id++"\n"); + }); + }); + } + },{ + ("Couldn't open file for writing: "++file).postln; + ^false; + }); + } + + readUnknownIDFromFile{ + arg unknowns; + var snpFile = File(unknowns, "r"), fileLength, line ="", outArr, counter = 0; + fileLength = (("wc -l "++unknowns.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace}); + fileLength.postln; + outArr = Array.new(fileLength[0].asInt); + if(snpFile.isOpen, { + protect{ + while{(line = snpFile.getLine).notNil }{ + outArr.add(line.asSymbol); + counter = counter + 1; + } + } + ^outArr; + },{ + ("Couldn't open file for writing: "++file).postln; + ^false; + }); + } +} |