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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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