From 839d8e3820c6097f89bdc096e264485d063c1943 Mon Sep 17 00:00:00 2001
From: David Runge <david.runge@frqrec.com>
Date: Tue, 14 Aug 2012 20:34:46 +0200
Subject: Classes and howto

---
 SNPFile.sc | 167 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 167 insertions(+)
 create mode 100644 SNPFile.sc

(limited to 'SNPFile.sc')

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;
+		});
+	}
+}
-- 
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