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

---
 SNPInfo.sc | 149 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 149 insertions(+)
 create mode 100644 SNPInfo.sc

(limited to 'SNPInfo.sc')

diff --git a/SNPInfo.sc b/SNPInfo.sc
new file mode 100644
index 0000000..26fc24a
--- /dev/null
+++ b/SNPInfo.sc
@@ -0,0 +1,149 @@
+SNPInfo{//helper class for calculations and constants used in the other classes
+	const <baseSingle = #[\A, \C, \G, \T];
+	const <basePair = #[\AA, \AC, \AG, \AT, \CC, \CG, \CT, \GG, \GT, \TT];
+	const <unknownBasePair = #[\AA, \CC, \GG, \TT];
+	const <emptyBasePair = #[\none, \none];
+	const <emptyBase = #[\none];
+//	const <chromosomesLength = #[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569];
+	const <chromosomesLength = #[247199719, 242751149, 199446827, 191263063, 180837866, 170896993, 158821424, 146274826, 140442298, 135374737, 134452384, 132289534, 114127980, 106360585, 100338915, 88822254, 78654742, 76117153, 63806651, 62435965, 46944323, 49528953, 154913754, 57741652, 16569];
+	const <chromosomesFactor = #[ 1, 1.0183256393155, 1.2394266818795, 1.2924592711349, 1.3669687907067, 1.4464837248482, 1.556463308124, 1.6899676161638, 1.7601514822835, 1.8260402529905, 1.8385670201281, 1.868626425126, 2.1659869823333, 2.324166597993, 2.4636475190109, 2.7830831561649, 3.142845716791, 3.2476217154365, 3.8741998698537, 3.9592519952242, 5.265806453317, 4.9910144274602, 1.5957247992325, 4.2811334701681, 14919.410887803 ];
+//	const <chromosomesFactor = #[1, 1.0248818404643, 1.2586989312271, 1.3039238578163, 1.3777202708052, 1.4566257978907, 1.5662480524924, 1.7029500665129, 1.7650631334069, 1.8390163889117, 1.8462117858074, 1.8621374094106, 2.1641997484794, 2.3218601681945, 2.4309688587862, 2.7585778581012, 3.0697700147583, 3.1923592004677, 4.2153713518124, 3.9547570730079, 5.1787069346401, 4.85825415617, 1.6052664523139, 4.1980065842769, 15043.190355483];
+	const <lengthAtOneMs = 69.236283611;//in hours
+	const <sCompany = #["ftdna-illumina", "23andme", "23andme-exome-vcf", "decodeme"];
+	const <a = #[1,0,0,0];
+	const <c = #[0,1,0,0];
+	const <g = #[0,0,1,0];
+	const <t = #[0,0,0,1];
+	const <e = #[0,0,0,0];
+	classvar <workingSCompany = #[1];//the companies working with this software (so far)
+
+	*calcPosition{//normalize all positions on chromosomes to the longest (the first) by chromosomesFactor of chromosomesFactor
+		arg chromosome, position;
+		var factor = 0.0, outPos = 0.0;
+		switch(chromosome.asSymbol,
+			\1,{factor = chromosomesFactor[0]},
+			\2,{factor = chromosomesFactor[1]},
+			\3,{factor = chromosomesFactor[2]},
+			\4,{factor = chromosomesFactor[3]},
+			\5,{factor = chromosomesFactor[4]},
+			\6,{factor = chromosomesFactor[5]},
+			\7,{factor = chromosomesFactor[6]},
+			\8,{factor = chromosomesFactor[7]},
+			\9,{factor = chromosomesFactor[8]},
+			\10,{factor = chromosomesFactor[9]},
+			\11,{factor = chromosomesFactor[10]},
+			\12,{factor = chromosomesFactor[11]},
+			\13,{factor = chromosomesFactor[12]},
+			\14,{factor = chromosomesFactor[13]},
+			\15,{factor = chromosomesFactor[14]},
+			\16,{factor = chromosomesFactor[15]},
+			\17,{factor = chromosomesFactor[16]},
+			\18,{factor = chromosomesFactor[17]},
+			\19,{factor = chromosomesFactor[18]},
+			\20,{factor = chromosomesFactor[19]},
+			\21,{factor = chromosomesFactor[20]},
+			\22,{factor = chromosomesFactor[21]},
+			\X,{factor = chromosomesFactor[22]},
+			\Y,{factor = chromosomesFactor[23]},
+			\MT,{factor = chromosomesFactor[24]}
+		);
+		^outPos = round(position.asFloat*factor);//round to the next possible slot
+	}
+	
+	*convertChromosome{//convert funky names of chromosomes to valid numbers
+		arg chrom;
+		switch(chrom,
+			\X, {^23},
+			\Y, {^24},
+			\MT,{^25},
+			"X", {^23},
+			"Y", {^24},
+			"MT",{^25},
+			{^chrom.asInt}
+		);
+	}
+	
+	*baseToVec{//calculate unique vectors on basis of the base given
+		arg base;
+		var out = [[],[]];
+		if(base.isArray, {//unwrap items in Array
+			base.do({
+				arg item, i;
+				if(item.notNil, {
+					out.put(i, this.baseToVec(item));
+				});
+			});
+			^out;
+		},{
+			if(this.isBasePair(base),{//if it's a base pair calc
+				switch(base,
+					\AA, {^a},
+					\AC, {^(a-c)},
+					\AG, {^(a-g)},
+					\AT, {^(a-t)},
+					\CC, {^c},
+					\CG, {^(c-g)},
+					\CT, {^(c-t)},
+					\GG, {^g},
+					\GT, {^(g-t)},
+					\TT, {^t},
+				);
+			},{
+				if(this.isBase(base),{//if it's a single base, return
+					switch(base,
+						\A, {^a},
+						\C, {^c},
+						\G, {^g},
+						\T, {^t}
+					);
+				},{
+					if(base == \none,{//if it's unknown, return empty
+						^e;
+					});
+				});
+			});
+		});
+	}
+
+
+	*createResolverForPair{//for known base pairs, create a resolver
+		arg base;
+		base = base.asSymbol;
+		switch(base,
+			\AC,{^[\AA, \CC]},
+			\AG,{^[\AA, \GG]},
+			\AT,{^[\AA, \TT]},
+			\CG,{^[\CC, \GG]},
+			\CT,{^[\CC, \TT]},
+			\GT,{^[\GG, \TT]},
+			{^[\none, \none]}
+		);
+	}
+
+	*isUnknownBasePair{//check if it's an unknown pair
+		arg base;
+		if(unknownBasePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+			^true;
+		},{
+			^false;
+		});
+	}
+
+	*isBase{//check if it's a single base
+		arg base;
+		if(baseSingle.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+			^true;
+		},{
+			^false;
+		});
+	}
+	
+	*isBasePair{//check if it's a (known) base pair
+		arg base;
+		if(basePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+			^true;
+		},{
+			^false;
+		});
+	}
+}
-- 
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