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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;
});
}
}
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