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

---
 SNPParser.sc | 107 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 SNPParser.sc

(limited to 'SNPParser.sc')

diff --git a/SNPParser.sc b/SNPParser.sc
new file mode 100644
index 0000000..d3e89e9
--- /dev/null
+++ b/SNPParser.sc
@@ -0,0 +1,107 @@
+SNPParser{
+	var <placement;
+	var <comboDict;
+	var <file;
+	var <fileLength;
+	var <userID;
+	var <testSet;
+
+	*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;
+		});
+		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}
+			);
+		});
+	}
+
+	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;
+	}
+}
-- 
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