diff options
| -rw-r--r-- | SNPInfo.sc | 283 |
1 files changed, 141 insertions, 142 deletions
@@ -1,155 +1,154 @@ 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]; + 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]; const <colorA = "#80ff00"; const <colorC = "#ff0000"; const <colorG = "#8000ff"; const <colorT = "#00ffff"; - classvar <workingSCompany = #[1];//the companies working with this software (so far) + 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; - }); - }); - }); - }); - } + *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} + ); + } - *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]} - ); - } + *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; + }); + }); + }); + }); + } - *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; - }); - } + *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]} + ); + } - *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; - }); - } + *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; + }); + } //returns a hex color value for a base/ base pair *getColorFromBase{ |