Repository 'kinatest_scoring_function'
hg clone https://toolshed.g2.bx.psu.edu/repos/jfb/kinatest_scoring_function

Changeset 0:ed9068208721 (2019-04-26)
Next changeset 1:876d4ca7289d (2019-04-27)
Commit message:
Uploaded
added:
scoring function/.RData
scoring function/.Rhistory
scoring function/Fisher-Char.csv
scoring function/Fisher-Table.csv
scoring function/KinatestFisherScoring.R
scoring function/KinatestScoring.xml
scoring function/output.csv
scoring function/screener.csv
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diff -r 000000000000 -r ed9068208721 scoring function/.RData
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Binary file scoring function/.RData has changed
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diff -r 000000000000 -r ed9068208721 scoring function/.Rhistory
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/.Rhistory Fri Apr 26 16:36:21 2019 -0400
[
b'@@ -0,0 +1,284 @@\n+install.packages("xlsx")\n+package("xlsx")\n+require(xlsx)\n+?read.xlsx\n+?read.xlsx("C:\\Users\\parkerlab\\Downloads\\ppse.xlsx")\n+?read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx")\n+figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx")\n+figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx",sheetIndex = 1)\n+setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin")\n+setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R\', echo=TRUE)\n+setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R\', echo=TRUE)\n+setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")\n+source(\'C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R\', echo=TRUE)\n+source(\'C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R\', echo=TRUE)\n+source(\'C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R\', echo=TRUE)\n+D835YFinalMatrix\n+FTLwtmotifs\n+DataFilename<-"stRequiredData.RData"\n+load(DataFilename)\n+setwd("F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Kinatest Fishertest/KT-ID fisher test")\n+load(DataFilename)\n+setwd("F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/ST fishertest/KT-ID fisher test")\n+load(DataFilename)\n+setwd("C:/Users/parkerlab/Downloads/stuff")\n+source(\'C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R\', echo=TRUE)\n+#put the names of your input files here\n+FirstSubstrateSet<- read.csv("Galaxy1071-(17A_TiO2_Substrates.csv).csv", stringsAsFactors=FALSE)\n+Firstsubbackfreq<- read.csv("Galaxy1072-(17A_TiO2_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE)\n+SecondSubstrateSet<- read.csv("Galaxy1073-(17A_FeNTA_Substrates.csv) (1).csv", stringsAsFactors=FALSE)\n+Secondsubbackfreq<- read.csv("Galaxy1074-(17A_FeNTA_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE)\n+#I should make an SOP for this.  Problems we encountered: no x in the xY motif, and the kilodemon\n+#the output files have both Y and xY, they shouldn\'t why is that happening?  make it not happen\n+#make sure that accession numbers stay locked to each motif, somehow\n+#output should look just like the KALIP input\n+#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps\n+FullMotifsOnly_questionmark<-"NO"\n+#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps\n+TruncatedMotifsOnly_questionmark<-"NO"\n+#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)\n+Are_You_Looking_For_Co'..b'ropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+Scores<-ThisKinGeneratedScores\n+Scores<-Scores*-1\n+order(scores)\n+order(Scores)\n+Scores[order(Scores)]\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+LynActive\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+source(\'F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R\', echo=TRUE)\n+args\n+toupper(6)\n+Positionm6<-"123kjhsdfk245                    23ddddd"\n+Positionm6<-toupper(M6)\n+M6<-"123kjhsdfk245                    23ddddd"\n+Positionm6<-toupper(M6)\n+Positionm6<-gsub("[^a-zA-Z]", "", Positionm6)\n+Positionm6<-unlist(strsplit(Positionm6,""))\n'
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diff -r 000000000000 -r ed9068208721 scoring function/Fisher-Char.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/Fisher-Char.csv Fri Apr 26 16:36:21 2019 -0400
b
b'@@ -0,0 +1,124 @@\n+"Normalization Score"\n+"0.144704867915654"\n+"Characterzation Table"\n+"threshold","Truepositives","Falsenegatives","Sensitivity","TrueNegatives","FalsePositives","One_Minus_Specificity","Accuracy","MCC","EER","Precision","FalsePositiveRate","F_One_Half","F_One","F_Two"\n+100,0,954,0,11793,0,0,92.5158860908449,NA,0.0748411390915509,NA,0,NA,NA,NA\n+99,0,954,0,11793,0,0,92.5158860908449,NA,0.0748411390915509,NA,0,NA,NA,NA\n+98,1,953,0.0010482180293501,11793,0,0,92.5237310739782,0.0311423230048369,0.0747626892602181,1,0,0.00626304801670146,0.00209424083769634,0.00130992926381975\n+97,11,943,0.0115303983228512,11793,0,0,92.6021809053111,0.103327941938382,0.0739781909468895,1,0,0.0661322645290581,0.0227979274611399,0.0143715704206951\n+96,24,930,0.0251572327044025,11793,0,0,92.7041656860438,0.152703439481177,0.0729583431395622,1,0,0.137142857142857,0.049079754601227,0.03125\n+95,37,917,0.0387840670859539,11793,0,0,92.8061504667765,0.1896994399291,0.071938495332235,1,0,0.201451905626134,0.0746720484359233,0.0480145341292499\n+94,49,905,0.0513626834381551,11793,0,0,92.9002902643759,0.21840789871475,0.0709970973562407,1,0,0.255652173913043,0.0977068793619143,0.0633893919793014\n+93,65,889,0.0681341719077568,11793,0,0,93.0258099945085,0.251710171649072,0.0697419000549149,1,0,0.321252059308072,0.127576054955839,0.0837413037876836\n+92,87,867,0.0911949685534591,11793,0,0,93.1983996234408,0.291461191104915,0.0680160037655919,1,0,0.400921658986175,0.167146974063401,0.111452728670254\n+91,101,853,0.105870020964361,11793,0,0,93.3082293873068,0.314211488490889,0.0669177061269318,1,0,0.446244477172312,0.191469194312796,0.128925197855502\n+90,114,840,0.119496855345912,11793,0,0,93.4102141680395,0.333992826795271,0.0658978583196046,1,0,0.485106382978723,0.213483146067416,0.145038167938931\n+89,125,829,0.131027253668763,11793,0,0,93.4965089825057,0.349887865156516,0.0650349101749431,1,0,0.515818431911967,0.231696014828545,0.158589190560771\n+88,144,810,0.150943396226415,11793,0,0,93.6455636620381,0.375822034999865,0.0635443633796187,1,0,0.564705882352941,0.262295081967213,0.181818181818182\n+87,164,790,0.171907756813417,11793,0,0,93.8024633247039,0.40139114523649,0.0619753667529615,1,0,0.611180124223602,0.293381037567084,0.206030150753769\n+86,173,781,0.181341719077568,11793,0,0,93.8730681729034,0.412405345125289,0.0612693182709657,1,0,0.630619684082625,0.307009760425909,0.216846327400351\n+85,187,767,0.19601677148847,11792,1,8.47960654625224e-05,93.9750529536362,0.427696010190806,0.0602494704636385,0.99468085106383,8.47960654625625e-05,0.65767878077374,0.327495621716287,0.233516483516484\n+84,198,756,0.207547169811321,11791,2,0.000169592130925156,94.053502784969,0.439099747221201,0.0594649721503099,0.99,0.000169592130925125,0.677309007981756,0.34315424610052,0.246513944223108\n+83,206,748,0.215932914046122,11791,2,0.000169592130925156,94.1162626500353,0.448126717902283,0.058837373499647,0.990384615384615,0.000169592130925125,0.692049272116461,0.354561101549053,0.25596421471173\n+82,221,733,0.231656184486373,11791,2,0.000169592130925156,94.2339373970346,0.464609640985605,0.057660626029654,0.991031390134529,0.000169592130925125,0.71830985915493,0.37553101104503,0.273582569943055\n+81,232,722,0.243186582809224,11790,3,0.000254388196387678,94.3123872283675,0.475197460606493,0.0568761277163254,0.987234042553191,0.000254388196387688,0.734952481520591,0.390243902439024,0.286349049617378\n+80,241,713,0.252620545073375,11790,3,0.000254388196387678,94.382992076567,0.484635721616722,0.0561700792343296,0.987704918032787,0.000254388196387688,0.749222797927461,0.402337228714524,0.29679802955665\n+79,250,704,0.262054507337526,11790,3,0.000254388196387678,94.4535969247666,0.493906981519595,0.0554640307523339,0.988142292490119,0.000254388196387688,0.762970498474059,0.414250207125104,0.307200786434013\n+78,259,695,0.271488469601677,11790,3,0.000254388196387678,94.5242017729662,0.503020490877378,0.0547579822703381,0.988549618320611,0.000254388196387688,0.77622377622377'..b'7,0.971698113207547,7932,3861,0.327397608750954,69.498705577783,0.350080954785325,0.30501294422217,0.193609022556391,0.327397608750954,0.276633840644584,0.322884012539185,0.538702928870293\n+0.9,931,23,0.975890985324948,7726,4067,0.344865598236242,67.9140189848592,0.340104369977249,0.320859810151408,0.186274509803922,0.344865598236242,0.266685763391578,0.312836021505376,0.528137054685727\n+0.8,934,20,0.979035639412998,7471,4322,0.366488594929195,65.937083235271,0.327437343758116,0.34062916764729,0.177701674277017,0.366488594929195,0.254982254982255,0.300805152979066,0.514770723104056\n+0.7,937,17,0.982180293501048,7209,4584,0.388705164080387,63.9052326037499,0.315159939373247,0.360947673962501,0.169715631226227,0.388705164080387,0.244031599965275,0.289420849420849,0.501767162900289\n+0.6,942,12,0.987421383647799,6897,4896,0.415161536504706,61.496822781831,0.302231669024383,0.38503177218169,0.161356628982528,0.415161536504706,0.23253517649963,0.277385159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b
diff -r 000000000000 -r ed9068208721 scoring function/Fisher-Table.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/Fisher-Table.csv Fri Apr 26 16:36:21 2019 -0400
b
b'@@ -0,0 +1,88 @@\n+"Fisher Odds, only significant ones"\n+"A",0.45340758779271,0.655627376365787,0.71057968549539,1,1,1,0.661475174634559,1,3.03585759888931,1.51459592041551,1,1.34017319444569,1,1,1\n+"C",0,0.345209441541176,1,0.439204781206491,1,1,0.352417894571245,1,1,1,1,1,1,1,1\n+"D",0.594344633886148,1,1,1,1.66384233276824,1,1,1,0.684008070280575,0.662015100187512,0.106442479722756,1,1,0.46316688049323,0.549966497154065\n+"E",0.292663597118304,0.583743651981213,0.68785363302483,1,1.73531930467867,1,1,1,1,0.699013291179544,0.250510064922151,0.570840777287419,0.578425718913143,0.463622230477107,0.346051999957002\n+"F",0.299928538715751,0.310436870652965,0.546211326676489,0.466014130557673,1,0.392669958184368,0.597097123689267,1,0.541570812223002,1,1,1,1,1,0.507835584012799\n+"G",0.507623945499749,0.560540490034444,0.593549904924849,1,1,1,0.60671232074634,1,1.769935997282,0.659419442533899,1,1.45462269351531,1,1,1\n+"H",1,1,1,1,1,1,2.50389609103775,1,1,1,1,1,1.65900481512235,1,1\n+"I",0.403090488413341,0.307889860478955,0.547600827640001,0.345511377655714,0.60283010288607,1,3.05823613451316,1,0.515194263689111,1,1,0.633369164396449,1,1,0.396867085826232\n+"K",1,1,1,1,1,0.458383240093005,0.1287096104636,1,0.701009912366299,0.288631636584031,0.455674501541205,1,1.35612696686909,1.55717575281757,1.76729652730069\n+"L",0.339323960452766,0.427863792799034,0.58257580990574,0.683316669661594,0.47870380329021,0.70501086022765,1.27917299735765,1,0.525203302996324,0.629753643787753,1.4239312668024,1,0.604968180719687,1,0.348509548422124\n+"M",0.118175538397184,1,1,1,0.452657007403625,0.475486293211633,0.521956307038838,1,1,1,1,1,1,1,1\n+"N",0.41425029242714,1,1,1,1,1,1,1,0.67828428617815,1.41228957959503,1,1,1.44652110748644,1,1\n+"P",0.577837665797938,0.549821083126844,1,1,1,1,0.64579936166802,1,0.045523732528101,1,2.94555559055344,1,1,1,1\n+"Q",0.518539374013132,1,1,1,1,1,1,1,1.79387423793372,1.74580554895124,0.418050638841107,1.52022365407306,1,1.48950328454724,1.7938685808038\n+"R",0.35739315300058,0.234281870411409,1,0.473603694865266,0.253577019829549,0.0961602178021488,0.112752320370177,1,0.624891558617653,0.244684557040745,0.652593952330456,1,1.532364865378,1.55521688109415,1.65583207772368\n+"S",0.653865883150467,1,0.686753635902289,1,1,1,0.383691710807265,1,1.44652913016801,1.77550892638296,1,1.57586881623192,1.37373064173574,1,1\n+"T",0.598575452086606,1,1,1,1,1.38585946627246,1,1,1,1.42838786961092,1,1.68907801656503,1,1,0.558290684266478\n+"V",0.421531121464353,1,1,0.388912326878284,0.593625698898935,1,2.05383252772703,1,0.628206316369443,1.90581441973588,1.51079096904443,1,1,0.567107694598072,1\n+"W",0,0,1,0,0.0920717790410791,0.137486618706072,0.172105344749846,1,0.330200515876214,1,1,1,1,1,1\n+"Y",0.0927835451424165,0.392260258007587,0.389966359737425,1,0.23839662456134,0.19308426038567,0.602131676639123,1,1,1,1,1,1,1,0.519682643132409\n+"O",1.62273665634627,1.55349187509736,1.55945112858584,1.50054591916817,1.43582150640241,1,0.340533394157341,1,1,1,0.590441361088773,0.631741799315981,0.814063968142815,1,1.16231438005455\n+"Fisher Odds"\n+"A",0.45340758779271,0.655627376365787,0.71057968549539,0.922214710541857,1.12643960007807,1.22199406131933,0.661475174634559,0,3.03585759888931,1.51459592041551,1.15534418367196,1.34017319444569,0.994904775595518,1.16836795794878,0.709896564912449\n+"C",0,0.345209441541176,1.00146440899469,0.439204781206491,0.480018086191882,0.997249605052092,0.352417894571245,0,1.32075646428044,0.955276553953329,0.563859656272759,1.2716137634101,0.841492271928643,0.78142523113654,0.672574792091774\n+"D",0.594344633886148,0.952808800174973,0.686928651324403,1.18868652765991,1.66384233276824,1.15692657056969,0.934463963606677,0,0.684008070280575,0.662015100187512,0.106442479722756,0.734519203364876,0.936217223907015,0.46316688049323,0.549966497154065\n+"E",0.292663597118304,0.583743651981213,0.68785363302483,1.1265094031077,1.73531930467867,1.07249791413733,1.13107495559908,0,0.96623246499136,0.699013291179544,0.2505100649221'..b'01549889,0.699471727050123,0.00160835273447844,0.00161298023901304,0.000783638443219455\n+"S",0.0378848082387598,0.151520967936582,0.0462577758847013,0.506589726042649,0.945478825334824,0.0588094656544786,2.20463037061022e-07,1,0.00151179017445491,5.44800282256041e-07,0.892809804343377,0.000399922851093616,0.0216134737623335,0.585941732405277,0.362403393344275\n+"T",0.0429530960125628,0.220179475135355,0.0604752858304872,0.354689914552864,0.348818971928349,0.0173283547087478,0.455308843282568,1,0.0888605301414739,0.0113200863172584,0.0780931954142391,0.0001935505172109,0.454024862825873,0.447117162435407,0.0134768353999804\n+"V",0.000260052098753436,0.933077986578566,0.241653207636216,6.97888616605839e-06,0.00190900627191319,0.837645429810913,1.60188499584885e-11,1,0.00352595402803889,3.58147791102221e-08,0.00134677266689915,0.882119394980568,0.677766779256124,0.00484159539185242,0.648690261650646\n+"W",0.0109893142652081,0.00728689130487901,0.564487211549605,0.00224725138308303,0.000659390138837808,0.0113761204032523,0.00186088444334728,1,0.0387341965379344,0.224592288864352,0.759664030669416,0.830535551065552,0.332630936109219,0.246997577410753,0.422660069424239\n+"Y",3.31354806515718e-07,0.00208059028589647,0.00120485550858747,0.113719479355765,3.33162802184648e-06,1.83736657151628e-07,0.0227590008460977,1,0.315092743244122,0.448253815185915,0.326649921610956,0.237389850772931,0.754913153305204,0.584040860397283,0.0305578672473756\n+"O",2.25632728914017e-21,3.6949906958159e-16,8.37849471964426e-15,1.28899811025089e-10,3.32927971024485e-07,0.166809153340628,1.18301196567235e-09,1,0.628908004932332,0.89828595937171,2.23789272589542e-06,4.60940778059626e-07,0.0063179507946423,0.70023863375871,0.0097508690921711\n+"Fisher p.values adjusted"\n+"A",0.122795413691055,1,1,1,1,1,1,1,2.343505438935e-28,0.151932736091851,1,1,1,1,1\n+"C",0.0450700269303707,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"D",1,1,1,1,0.0496251402511549,1,1,1,1,1,2.18574943514167e-11,1,1,0.203273958741314,1\n+"E",0.00144988434702009,1,1,1,0.000744001010330062,1,1,1,1,1,1.29432305369892e-08,0.750592195929664,0.549331971016308,0.0449007103952895,0.00169424013454612\n+"F",0.0614619353863486,0.113630122058304,1,0.359402483241389,1,0.211404778760815,1,1,0.880723393891192,1,1,1,1,1,1\n+"G",0.583976256767124,0.742455219718913,1,1,1,1,0.309563250083629,1,7.69659521897839e-06,1,1,0.938412089161546,1,1,1\n+"H",1,1,1,1,1,1,7.00044987883364e-07,1,1,1,1,1,1,1,1\n+"I",0.273140699310654,0.0112797955547782,1,0.00405401931171288,1,1,4.78348513257024e-27,1,0.128302414272547,1,1,1,1,1,0.207984619188537\n+"K",1,1,1,1,1,1,0.000172658632597143,1,1,9.47114852976229e-07,0.010684458976269,1,1,0.48017877905658,0.0100857887572787\n+"L",1.67589166481447e-05,0.00238563201824836,0.403223717820169,1,0.000549958124231666,1,1,1,0.00240531013034325,0.514612545179084,0.240854209082961,1,0.990940968985578,1,9.7443341282722e-05\n+"M",0.00575874540560851,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"N",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+"P",1,1,1,1,1,1,1,1,2.51813533606161e-13,1,1.27762624149995e-22,1,1,1,1\n+"Q",1,1,1,1,1,1,1,1,0.0031851196429891,0.0127122716286365,0.0623357876626607,1,1,1,0.173026790739019\n+"R",1,0.989827443559247,1,1,0.06923453969436,0.000221353464359228,0.00279119425734096,1,1,9.86616899750547e-08,1,1,0.50663111136071,0.508088775289108,0.246846109614128\n+"S",1,1,1,1,1,1,6.94458566742219e-05,1,0.476213904953298,0.000171612088910653,1,0.125975698094489,1,1,1\n+"T",1,1,1,1,1,1,1,1,1,1,1,0.0609684129214335,1,1,1\n+"V",0.0819164111073322,1,1,0.00219834914230839,0.601336975652656,1,5.04593773692388e-09,1,1,1.128165541972e-05,0.424233390073231,1,1,1,1\n+"W",1,1,1,0.707884185671155,0.207707893733909,1,0.586178599654394,1,1,1,1,1,1,1,1\n+"Y",0.000104376764052451,0.655385940057387,0.379529485205053,1,0.00104946282688164,5.78770470027627e-05,1,1,1,1,1,1,1,1,1\n+"O",7.10743096079153e-19,1.16392206918201e-13,2.63922583668794e-12,4.0603440472903e-08,0.000104872310872713,1,3.7264876918679e-07,1,1,1,0.000704936208657058,0.000145196345088782,1,1,1\n'
b
diff -r 000000000000 -r ed9068208721 scoring function/KinatestFisherScoring.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/KinatestFisherScoring.R Fri Apr 26 16:36:21 2019 -0400
[
b'@@ -0,0 +1,1261 @@\n+# system.time({\r\n+\r\n+args = commandArgs(trailingOnly=TRUE)\r\n+TodaysKinase<-as.character(args[1])\r\n+\r\n+CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE)\r\n+ThisKinSheet<-read.csv("Fisher-Table.csv", header=FALSE, stringsAsFactors=FALSE)\r\n+NormalizationScore<-CharTable[2,1]\r\n+\r\n+#so here\'s the question, do I want this file to be able to score using any EPM table as well? I guess I have to.\r\n+\r\n+\r\n+\r\n+\r\n+M6<-args[2]\r\n+M5<-args[3]\r\n+M4<-args[4]\r\n+M3<-args[5]\r\n+M2<-args[6]\r\n+M1<-args[7]\r\n+D0<-args[8]\r\n+P1<-args[9]\r\n+P2<-args[10]\r\n+P3<-args[11]\r\n+P4<-args[12]\r\n+P5<-args[13]\r\n+P6<-args[14]\r\n+\r\n+\r\n+A=1\r\n+C=2\r\n+D=3\r\n+E=4\r\n+F=5\r\n+G=6\r\n+H=7\r\n+I=8\r\n+K=9\r\n+L=10\r\n+M=11\r\n+N=12\r\n+P=13\r\n+Q=14\r\n+R=15\r\n+S=16\r\n+T=17\r\n+V=18\r\n+W=19\r\n+Y=20\r\n+aa_props <- c("A"=A, "C"=C, "D"=D, "E"=E, "F"=F,"G"=G,"H"=H,"I"=I,"K"=K,"L"=L,"M"=M,"N"=N,"P"=P,"Q"=Q,"R"=R,\r\n+              "S"=S,"T"=T,"V"=V,"W"=W,"Y"=Y,"xY"=Y,"O"=21)\r\n+Positionm6<-gsub("[^a-zA-Z]", "", M6)\r\n+Positionm6<-toupper(Positionm6)\r\n+Positionm6<-unlist(strsplit(Positionm6,""))\r\n+Positionm6<-sapply(Positionm6, function(x) aa_props[x])\r\n+\r\n+Positionm5<-gsub("[^a-zA-Z]", "", M5)\r\n+Positionm5<-toupper(Positionm5)\r\n+Positionm5<-unlist(strsplit(Positionm5,""))\r\n+Positionm5<-sapply(Positionm5, function(x) aa_props[x])\r\n+\r\n+Positionm4<-gsub("[^a-zA-Z]", "", M4)\r\n+Positionm4<-toupper(Positionm4)\r\n+Positionm4<-unlist(strsplit(Positionm4,""))\r\n+Positionm4<-sapply(Positionm4, function(x) aa_props[x])\r\n+\r\n+Positionm3<-gsub("[^a-zA-Z]", "", M3)\r\n+Positionm3<-toupper(Positionm3)\r\n+Positionm3<-unlist(strsplit(Positionm3,""))\r\n+Positionm3<-sapply(Positionm3, function(x) aa_props[x])\r\n+\r\n+Positionm2<-gsub("[^a-zA-Z]", "", M2)\r\n+Positionm2<-toupper(Positionm2)\r\n+Positionm2<-unlist(strsplit(Positionm2,""))\r\n+Positionm2<-sapply(Positionm2, function(x) aa_props[x])\r\n+\r\n+Positionm1<-gsub("[^a-zA-Z]", "", M1)\r\n+Positionm1<-toupper(Positionm1)\r\n+Positionm1<-unlist(strsplit(Positionm1,""))\r\n+Positionm1<-sapply(Positionm1, function(x) aa_props[x])\r\n+\r\n+Positiond0<-gsub("[^a-zA-Z]", "", D0)\r\n+Positiond0<-toupper(Positiond0)\r\n+Positiond0<-unlist(strsplit(Positiond0,""))\r\n+Positiond0<-sapply(Positiond0, function(x) aa_props[x])\r\n+\r\n+Positionp1<-gsub("[^a-zA-Z]", "", P1)\r\n+Positionp1<-toupper(Positionp1)\r\n+Positionp1<-unlist(strsplit(Positionp1,""))\r\n+Positionp1<-sapply(Positionp1, function(x) aa_props[x])\r\n+\r\n+Positionp2<-gsub("[^a-zA-Z]", "", P2)\r\n+Positionp2<-toupper(Positionp2)\r\n+Positionp2<-unlist(strsplit(Positionp2,""))\r\n+Positionp2<-sapply(Positionp2, function(x) aa_props[x])\r\n+\r\n+Positionp3<-gsub("[^a-zA-Z]", "", P3)\r\n+Positionp3<-toupper(Positionp3)\r\n+Positionp3<-unlist(strsplit(Positionp3,""))\r\n+Positionp3<-sapply(Positionp3, function(x) aa_props[x])\r\n+\r\n+Positionp4<-gsub("[^a-zA-Z]", "", P4)\r\n+Positionp4<-toupper(Positionp4)\r\n+Positionp4<-unlist(strsplit(Positionp4,""))\r\n+Positionp4<-sapply(Positionp4, function(x) aa_props[x])\r\n+\r\n+Positionp5<-gsub("[^a-zA-Z]", "", P5)\r\n+Positionp5<-toupper(Positionp5)\r\n+Positionp5<-unlist(strsplit(Positionp5,""))\r\n+Positionp5<-sapply(Positionp5, function(x) aa_props[x])\r\n+\r\n+Positionp6<-gsub("[^a-zA-Z]", "", P6)\r\n+Positionp6<-toupper(Positionp6)\r\n+Positionp6<-unlist(strsplit(Positionp6,""))\r\n+Positionp6<-sapply(Positionp6, function(x) aa_props[x])\r\n+\r\n+\r\n+\r\n+\r\n+#what the below code does is stupid.  I need to make a combinatorial library of peptides and then calculate their values\r\n+#but each peptide needs a value calculated for every different kinase.  So I first make it so that every AA at every position is labelled differently\r\n+#IE an A at position negative 6 is called m6a (minus 6 Alanine)\r\n+#then further on I replace valued like m6a with whatever value is found in the EPM table for both this kinase and every other kinase\r\n+#then I will multiply those values together\r\n+\r\n+if(2==2){\r\n+aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N",\r\n+               "13"="P'..b'eratedScores,YesNormColumn)\r\n+YesGeneratedScores<-as.data.frame(YesGeneratedScores)\r\n+YesGeneratedScores<-with(YesGeneratedScores, 100*V1/(V1+V2))\r\n+\r\n+FLT3GeneratedScores<-as.matrix(FLT3GeneratedScores, ncol=1)\r\n+FLT3Norm<-FLT3Norm<-1/as.numeric(FLT3[22,1])\r\n+FLT3NormColumn<-as.matrix(rep(FLT3Norm,times=nrow(FLT3GeneratedScores)),ncol=1)\r\n+FLT3GeneratedScores<-cbind(FLT3GeneratedScores,FLT3NormColumn)\r\n+FLT3GeneratedScores<-as.data.frame(FLT3GeneratedScores)\r\n+FLT3GeneratedScores<-with(FLT3GeneratedScores, 100*V1/(V1+V2))\r\n+\r\n+ALKGeneratedScores<-as.matrix(ALKGeneratedScores, ncol=1)\r\n+ALKNorm<-ALKNorm<-1/as.numeric(ALK[22,1])\r\n+ALKNormColumn<-as.matrix(rep(ALKNorm,times=nrow(ALKGeneratedScores)),ncol=1)\r\n+ALKGeneratedScores<-cbind(ALKGeneratedScores,ALKNormColumn)\r\n+ALKGeneratedScores<-as.data.frame(ALKGeneratedScores)\r\n+ALKGeneratedScores<-with(ALKGeneratedScores, 100*V1/(V1+V2))\r\n+\r\n+ThisKinGeneratedScores1<-as.matrix(ThisKinGeneratedScores, ncol=1)\r\n+ThisKinNorm<-ThisKinNorm<-1/as.numeric(NormalizationScore)\r\n+ThisKinNormColumn<-as.matrix(rep(ThisKinNorm,times=nrow(ThisKinGeneratedScores1)),ncol=1)\r\n+ThisKinGeneratedScores1<-cbind(ThisKinGeneratedScores1,ThisKinNormColumn)\r\n+ThisKinGeneratedScores1<-as.data.frame(ThisKinGeneratedScores1)\r\n+ThisKinGeneratedScores1<-with(ThisKinGeneratedScores1, V1/(V1+V2))\r\n+\r\n+AblThresh<-as.numeric(Abl[24,1])\r\n+AblActive<-unlist(AblGeneratedScores)>AblThresh/100\r\n+ArgThresh<-as.numeric(Arg[24,1])\r\n+ArgActive<-unlist(ArgGeneratedScores)>ArgThresh/100\r\n+BtkThresh<-as.numeric(Btk[24,1])\r\n+BtkActive<-unlist(BtkGeneratedScores)>BtkThresh/100\r\n+CskThresh<-as.numeric(Csk[24,1])\r\n+CskActive<-(CskGeneratedScores)>CskThresh/100\r\n+FynThresh<-as.numeric(Fyn[24,1])\r\n+FynActive<-unlist(FynGeneratedScores)>FynThresh/100\r\n+HckThresh<-as.numeric(Hck[24,1])\r\n+HckActive<-unlist(HckGeneratedScores)>HckThresh/100\r\n+JAK2Thresh<-as.numeric(JAK2[24,1])\r\n+JAk2Active<-unlist(JAK2GeneratedScores)>JAK2Thresh/100\r\n+LckThresh<-as.numeric(Lck[24,1])\r\n+LckActive<-unlist(LckGeneratedScores)>LckThresh/100\r\n+LynThresh<-as.numeric(Lyn[24,1])\r\n+LynActive<-unlist(LynGeneratedScores)>LynThresh/100\r\n+Pyk2Thresh<-as.numeric(Pyk2[24,1])\r\n+Pyk2Active<-unlist(Pyk2GeneratedScores)>Pyk2Thresh/100\r\n+SrcThresh<-as.numeric(Src[24,1])\r\n+SrcActive<-unlist(SrcGeneratedScores)>SrcThresh/100\r\n+SykThresh<-as.numeric(Syk[24,1])\r\n+SykActive<-unlist(SykGeneratedScores)>SykThresh/100\r\n+YesThresh<-as.numeric(Yes[24,1])\r\n+YesActive<-unlist(YesGeneratedScores)>YesThresh/100\r\n+ALKThresh<-as.numeric(ALK[24,1])\r\n+ALKActive<-unlist(ALKGeneratedScores)>ALKThresh/100\r\n+FLT3Thresh<-as.numeric(FLT3[24,1])\r\n+FLT3Active<-unlist(FLT3GeneratedScores)>FLT3Thresh/100\r\n+\r\n+\r\n+AllActive<-AblActive+ArgActive+BtkActive+CskActive+FynActive+HckActive+JAk2Active+LckActive+LynActive+Pyk2Active+SrcActive+SykActive+YesActive+ALKActive+FLT3Active\r\n+Scores<-ThisKinGeneratedScores\r\n+ThresholdValues<-ThisKinGeneratedScores1\r\n+\r\n+FullMotifs<-rep("Z",times=nrow(GeneratedPeptides))\r\n+for (i in 1:nrow(GeneratedPeptides)) {\r\n+  motif<-GeneratedPeptides[i,1:13]\r\n+  motif<-paste(motif,sep = "", collapse = "")\r\n+  FullMotifs[i]<-motif\r\n+}\r\n+\r\n+Scores<-1/Scores\r\n+\r\n+PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)\r\n+\r\n+PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)\r\n+RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,\r\n+                                       PeptidesWithRanks$Scores,\r\n+                                       decreasing = FALSE),]\r\n+\r\n+RanksPeptides$Scores<-1/RanksPeptides$Scores\r\n+\r\n+#RanksPeptides$Scores<-1/RanksPeptides$Scores\r\n+\r\n+#I want to see how much of the sequence space we still have available.  I should do so\r\n+\r\n+write.table(RanksPeptides,file = "output.csv",append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")\r\n+\r\n+# })\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r ed9068208721 scoring function/KinatestScoring.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/KinatestScoring.xml Fri Apr 26 16:36:21 2019 -0400
[
@@ -0,0 +1,49 @@
+<tool id="kinatestid_fisher_scoring" name="Scoring function for KINATEST-ID" version="50.5.0">
+    <description>determine if peptides will be phosphorylated</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+        ln -s '$FisherTable' Fisher-Char.csv && 
+        ln -s '$CharacterizationTable' Fisher-Table.csv && 
+        Rscript '$__tool_directory__/KinatestFisherScoring.R' outGroup
+    ]]></command>
+    <inputs>
+        <param format="csv" name="FisherTable" type="data" label="Fisher Odds Table output"/>
+        <param format="csv" name="CharacterizationTable" type="data" label="Characterization Table Output"/>
+ <param name="M6" type="text" value="ACD" label="Amino Acid(s) in -6 Position"/>
+ <param name="M5" type="text" value="EFG" label="Amino Acid(s) in -5 Position"/>
+ <param name="M4" type="text" value="HIK" label="Amino Acid(s) in -4 Position"/>
+ <param name="M3" type="text" value="LMN" label="Amino Acid(s) in -3 Position"/>
+ <param name="M2" type="text" value="PQR" label="Amino Acid(s) in -2 Position"/>
+ <param name="M1" type="text" value="STV" label="Amino Acid(s) in -1 Position"/>
+ <param name="D0" type="text" value="Y" label="Amino Acid(s) in Central Position"/>
+ <param name="P1" type="text" value="VTS" label="Amino Acid(s) in +1 Position"/>
+ <param name="P2" type="text" value="RQP" label="Amino Acid(s) in +2 Position"/>
+ <param name="P3" type="text" value="NML" label="Amino Acid(s) in +3 Position"/>
+ <param name="P4" type="text" value="KIH" label="Amino Acid(s) in +4 Position"/>
+ <param name="P5" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/>
+ <param name="P6" type="text" value="DCA" label="Amino Acid(s) in +6 Position"/>
+ <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="PeptidesWithScores" from_work_dir="output.csv" label="${outGroup}_Substrates and Scores"/>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    
+    <help><![CDATA[
+
+
+This tool is intended for use in conjunction with a Kinamine tool and a Negative Motif Finder tool.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates the kinases preferred substrate motif.
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1074/mcp.RA118.001111</citation>
+    </citations>
+</tool>
+
b
diff -r 000000000000 -r ed9068208721 scoring function/output.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/output.csv Fri Apr 26 16:36:21 2019 -0400
b
@@ -0,0 +1,21 @@
+"FullMotifs","1","2","3","4","5","6","7","8","9","10","11","12","13","Scores","ThresholdValues","AllActive","AblActive","ArgActive","BtkActive","CskActive","FynActive","HckActive","JAk2Active","LckActive","LynActive","Pyk2Active","SrcActive","SykActive","YesActive"
+"DCEQRVYPYEHIC","D","C","E","Q","R","V","Y","P","Y","E","H","I","C",0.0022522858511427,0.000325810539493378,6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"SCEQRVYPYEHIC","S","C","E","Q","R","V","Y","P","Y","E","H","I","C",0.0022522858511427,0.000325810539493378,6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"ACEQRVYPYEHIC","A","C","E","Q","R","V","Y","P","Y","E","H","I","C",0.00147666026341047,0.000213634279015669,6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"CCEQRVYPYEHIC","C","C","E","Q","R","V","Y","P","Y","E","H","I","C",0.000777510340864064,0.000112496874207213,6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"FCEQRVYPYEHIC","F","C","E","Q","R","V","Y","P","Y","E","H","I","C",0.00069919257144469,0.000101166333036066,6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"DCEQRVYPYRHIC","D","C","E","Q","R","V","Y","P","Y","R","H","I","C",0.00586734160095303,0.000848312646043264,7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"SCEQRVYPYRHIC","S","C","E","Q","R","V","Y","P","Y","R","H","I","C",0.00586734160095303,0.000848312646043264,7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"ACEQRVYPYRHIC","A","C","E","Q","R","V","Y","P","Y","R","H","I","C",0.00384678978007467,0.000556339521071752,7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"DCEQRVYPYEGIC","D","C","E","Q","R","V","Y","P","Y","E","G","I","C",0.00327622611135562,0.000473861215800341,7,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"SCEQRVYPYEGIC","S","C","E","Q","R","V","Y","P","Y","E","G","I","C",0.00327622611135562,0.000473861215800341,7,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"ACEQRVYPYEGIC","A","C","E","Q","R","V","Y","P","Y","E","G","I","C",0.00214798352976917,0.000310727091624341,7,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"CCEQRVYPYRHIC","C","C","E","Q","R","V","Y","P","Y","R","H","I","C",0.0020254617173963,0.000293008291262032,7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"FCEQRVYPYRHIC","F","C","E","Q","R","V","Y","P","Y","R","H","I","C",0.00182143916565182,0.000263501662455362,7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"CCEQRVYPYEGIC","C","C","E","Q","R","V","Y","P","Y","E","G","I","C",0.00113098418626369,0.000163632137429536,7,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"FCEQRVYPYEGIC","F","C","E","Q","R","V","Y","P","Y","E","G","I","C",0.00101706138156077,0.000147152075960544,7,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE
+"DCEQRVYPYRGIC","D","C","E","Q","R","V","Y","P","Y","R","G","I","C",0.00853476824335272,0.00123349911217382,9,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,TRUE
+"SCEQRVYPYRGIC","S","C","E","Q","R","V","Y","P","Y","R","G","I","C",0.00853476824335272,0.00123349911217382,9,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,TRUE
+"ACEQRVYPYRGIC","A","C","E","Q","R","V","Y","P","Y","R","G","I","C",0.00559562771127938,0.000809059461632694,9,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,TRUE
+"CCEQRVYPYRGIC","C","C","E","Q","R","V","Y","P","Y","R","G","I","C",0.00294628257897116,0.000426159741877843,9,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,TRUE
+"FCEQRVYPYRGIC","F","C","E","Q","R","V","Y","P","Y","R","G","I","C",0.00264950674521472,0.000383249587048582,9,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,TRUE
b
diff -r 000000000000 -r ed9068208721 scoring function/screener.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/screener.csv Fri Apr 26 16:36:21 2019 -0400
b
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