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4
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1 FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE, header = FALSE)
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2 Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
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3 SubstrateHeader<-FirstSubstrateSet[1,]
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4 FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
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5 if(nrow(Firstsubbackfreq[1,]>35)){
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6 if(grepl(pattern = "Properties", x=Firstsubbackfreq[1,22])){
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7 Firstsubbackfreq<-t(Firstsubbackfreq)
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8 }
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9 }
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10
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11
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12 SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE, header = FALSE)
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13 Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
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14 SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
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15 if(nrow(Secondsubbackfreq[1,]>35)){
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16 if(grepl(pattern = "Properties", x=Secondsubbackfreq[1,22])){
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17 Secondsubbackfreq<-t(Secondsubbackfreq)
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18 }
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19 }
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20
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21
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22 ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE, header = FALSE)
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23 Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
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24 ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
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25 if(nrow(Thirdsubbackfreq[1,]>35)){
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26 if(grepl(pattern = "Properties", x=Thirdsubbackfreq[1,22])){
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27 Thirdsubbackfreq<-t(Thirdsubbackfreq)
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28 }
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29 }
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30
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31 #the above three sections bring in the input files and ensure they are properly aligned. The if statements align them if they are misaligned
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32
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33 First_unshared_motifs_table<-"R1 substrates.csv"
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34 First_unshared_subbackfreq<-"R1 SBF.csv"
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35
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36 Second_unshared_motifs_table<-"R2 subs.csv"
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37 Second_unshared_subbackfreq<-"R2 SBf.csv"
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38
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39 Third_unshared_motifs_table<-"R3 subs.csv"
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40 Third_unshared_subbackfreq<-"R3 SBF.csv"
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41
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42 #the above 4 sections create the names of the output files that this tool can create
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43
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44
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45
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46
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47 FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
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48 FirstSubstrateSet[,11]<-FirstxY
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49
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50 SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
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51 SecondSubstrateSet[,11]<-SecondxY
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52
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53 ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
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54 ThirdSubstrateSet[,11]<-ThirdxY
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55
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56 #for each input file, mark the phospho-Tyrosine (which is always housed in column 11)
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57 #with an xY to denote that is it a phospho and not regular tyrosine
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58
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59
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60 #currently the substrates are a dataframe with many values, I want to collapse each substrate into a single variable,
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61 #but if I simply use the paste() function then I lose any information about whether the substrate was truncated on the C or N terminal.
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62 #so the for loops below then are constructed so as to retain that information on how any substrate is truncated.
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63
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64 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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65 FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1)
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66 #create the vectors which will house the first set of substrates and the first set of accession numbers
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67
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68
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69 for (i in 1:nrow(FirstSubstrateSet)){
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70 FTLwtletters<-FirstSubstrateSet[i,4:18]
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71 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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72 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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73 leftspaces<-c()
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74 rightspaces<-c()
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75
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76 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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77 YYYposition <- match(x = "x", table = YYYmotif)
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78 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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79 #just 3 letters to the left of x
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80
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81 YYYLettersToTheLeft <- YYYposition - 1
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82 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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83 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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84 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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85
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86
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87
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88 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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89 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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90 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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91 #add blank spaces if the motif has less than 4 letters to the left/right
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92 motif<-c(leftspaces,YYYmotif,rightspaces)
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93 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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94 motif<-motif[!motif %in% "x"]
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95 motif<-paste(motif, sep="", collapse="")
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96 FTLwtletters<-motif
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97 FTLwtmotifs[i,1]<-FTLwtletters
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98 }
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99
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100 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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101 motif<-YYYmotif
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102 #add blank spaces if the motif has less than 4 letters to the left/right
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103 motif<-c(leftspaces,YYYmotif,rightspaces)
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104 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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105 motif<-motif[!motif %in% "x"]
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106 motif<-paste(motif, sep="", collapse="")
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107 FTLwtletters<-motif
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108 FTLwtmotifs[i,1]<-FTLwtletters
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109 }
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110 }
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111
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112 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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113 D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1)
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114 #vectors to house the second set of substrates and accession numbers
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115
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116 for (i in 1:nrow(SecondSubstrateSet)){
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117 D835letters<-SecondSubstrateSet[i,4:18]
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118 D835letters<-D835letters[D835letters !="XXXXX"]
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119 D835letters<-paste(D835letters, sep="", collapse="")
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120 leftspaces<-c()
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121 rightspaces<-c()
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122
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123 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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124 YYYposition <- match(x = "x", table = YYYmotif)
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125 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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126 #just 3 letters to the left of x
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127
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128 YYYLettersToTheLeft <- YYYposition - 1
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129 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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130 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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131 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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132 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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133 #variable the user puts in is
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134 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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135 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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136 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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137 #add blank spaces if the motif has less than 4 letters to the left/right
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138 motif<-c(leftspaces,YYYmotif,rightspaces)
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139 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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140 motif<-motif[!motif %in% "x"]
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141 motif<-paste(motif, sep="", collapse="")
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142 D835letters<-motif
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143 D835Ymotifs[i,1]<-D835letters
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144 }
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145
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146 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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147 motif<-YYYmotif
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148 #add blank spaces if the motif has less than 4 letters to the left/right
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149 motif<-c(leftspaces,YYYmotif,rightspaces)
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150 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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151 motif<-motif[!motif %in% "x"]
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152 motif<-paste(motif, sep="", collapse="")
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153 D835letters<-motif
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154 D835Ymotifs[i,1]<-D835letters
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155 }
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156 }
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157
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158
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159 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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160 ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
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161 #third set of substrates and accession numbers
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162
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163
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164 for (i in 1:nrow(ThirdSubstrateSet)){
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165 ITDletters<-ThirdSubstrateSet[i,4:18]
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166 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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167 ITDletters<-paste(ITDletters, sep="", collapse="")
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168 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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169 leftspaces<-c()
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170 rightspaces<-c()
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171 YYYposition <- match(x = "x", table = YYYmotif)
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172 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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173 #just 3 letters to the left of x
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174
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175 YYYLettersToTheLeft <- YYYposition - 1
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176 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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177 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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178 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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179 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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180 #variable the user puts in is
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181 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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182 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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183 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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184 #add blank spaces if the motif has less than 4 letters to the left/right
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185 motif<-c(leftspaces,YYYmotif,rightspaces)
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186 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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187 motif<-motif[!motif %in% "x"]
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188 motif<-paste(motif, sep="", collapse="")
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189 ITDletters<-motif
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190 ITDmotifs[i,1]<-ITDletters
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191 # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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192 }
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193
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194 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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195 motif<-YYYmotif
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196 #add blank spaces if the motif has less than 4 letters to the left/right
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197 motif<-c(leftspaces,YYYmotif,rightspaces)
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198 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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199 motif<-motif[!motif %in% "x"]
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200 motif<-paste(motif, sep="", collapse="")
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201 ITDletters<-motif
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202 ITDmotifs[i,1]<-ITDletters
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203 # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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204 }
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205 }
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206
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207
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208 SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
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209 SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
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210 SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
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211 #this tool is essentially looking for the intersection of three sets, and to do so it performs 1 intersection at a time
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212 #this find the intersection of the substrate sets
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213
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214 AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
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215 AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
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216 AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
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217 #this tool is essentially looking for the intersection of three sets, and to do so it performs 1 intersection at a time
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218 #this find the intersection of the accession number sets
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219
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220
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221 for (x in 1:length(AccessionOverlapFinal)) {
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222 for (y in 1:ncol(Firstsubbackfreq)) {
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223 Acc<-AccessionOverlapFinal[x]
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224 SBF<-Firstsubbackfreq[1,y]
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225 if(Acc==SBF){
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226 FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
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227 }
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228 }
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229 }
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230 #for every accession number, go back to the original substrate background frequency file and find the protein statistics associated with that number
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231 #columnbind all those protein statistics together
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232 FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
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233
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234
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235 #write all files, in the proper format so that the files coming out look like the files coming in
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236
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237 if(grepl(pattern = "Properties", x=FinalMatrix[22,1])==FALSE){
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238 Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
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239 write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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240 } else {
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241 write.table(x=FinalMatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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242 }
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243
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244 SubstrateMatrix<-SubstrateHeader
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245 if(ncol(SubstrateMatrix)>18){
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246 SubstrateMatrix<-SubstrateMatrix[,1:18]
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247 }
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248
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249 for (z in 1:length(SubstrateOverlapFINAL)) {
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250 motif<-SubstrateOverlapFINAL[z]
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251 newmotif<-unlist(strsplit(motif,split = ""))
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252
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253 Addition<-""
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254 outputmotif<-c(Addition,Addition,Addition,newmotif)
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255 SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
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256 }
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257 write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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