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2
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1 FirstSubstrateSet<- read.csv("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
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2 Firstsubbackfreq<- read.csv("r1sbf.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("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
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13 Secondsubbackfreq<- read.csv("r1sbf.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("r2sub.csv", stringsAsFactors=FALSE, header = FALSE)
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23 Thirdsubbackfreq<- read.csv("r2sbf.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
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32
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33
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34 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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35 FullMotifsOnly_questionmark<-"NO"
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36 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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37 TruncatedMotifsOnly_questionmark<-"NO"
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38 #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)
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39 Are_You_Looking_For_Commonality<-"YES"
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40
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41
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42 #then put the names of your output files here
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43 Shared_motifs_table<-"sharedmotifs.csv"
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44 Shared_subbackfreq_table<-"sharedSBF.csv"
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45
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46 # Shared_motifs_table<-"Shared motifs 7-27-17.csv"
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47 # Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
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48
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49 First_unshared_motifs_table<-"R1 substrates.csv"
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50 First_unshared_subbackfreq<-"R1 SBF.csv"
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51
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52 Second_unshared_motifs_table<-"R2 subs.csv"
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53 Second_unshared_subbackfreq<-"R2 SBf.csv"
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54
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55 Third_unshared_motifs_table<-"R3 subs.csv"
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56 Third_unshared_subbackfreq<-"R3 SBF.csv"
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57
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58 #final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around
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59 #other languages to see if any of them can do it.
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60 ####################################################################################################################################
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61
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62
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63
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64
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65
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66 FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
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67 FirstSubstrateSet[,11]<-FirstxY
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68
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69 SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
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70 SecondSubstrateSet[,11]<-SecondxY
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71
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72 ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
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73 ThirdSubstrateSet[,11]<-ThirdxY
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74
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75
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76
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77
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78
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79
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80
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81
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82
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83
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84
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85 ####################################################################################################################################
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86 ####################################################################################################################################
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87 # better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two
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88 # separate proteins thus two separate accession numbers?
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89 # It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second
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90 # accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
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91 ####################################################################################################################################
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92 ####################################################################################################################################
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93 ####################################################################################################################################
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94 ####################################################################################################################################
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95
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96 #Create the motif sets, deciding wether or not you're looking for truncated or full here
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97 #full only
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98
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99 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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100 FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1)
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101
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102 for (i in 1:nrow(FirstSubstrateSet)){
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103 FTLwtletters<-FirstSubstrateSet[i,4:18]
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104 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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105 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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106 leftspaces<-c()
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107 rightspaces<-c()
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108
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109 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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110 YYYposition <- match(x = "x", table = YYYmotif)
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111 #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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112 #just 3 letters to the left of x
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113
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114 YYYLettersToTheLeft <- YYYposition - 1
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115 #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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116 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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117 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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118 #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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119 #variable the user puts in is
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120
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121
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122 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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123 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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124 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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125 #add blank spaces if the motif has less than 4 letters to the left/right
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126 motif<-c(leftspaces,YYYmotif,rightspaces)
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127 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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128 motif<-motif[!motif %in% "x"]
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129 motif<-paste(motif, sep="", collapse="")
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130 FTLwtletters<-motif
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131 FTLwtmotifs[i,1]<-FTLwtletters
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132 # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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133 }
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134
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135 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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136 motif<-YYYmotif
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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 FTLwtletters<-motif
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143 FTLwtmotifs[i,1]<-FTLwtletters
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144 # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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145
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146
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147 }
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148
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149 }
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150
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151 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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152 D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1)
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153
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154 for (i in 1:nrow(SecondSubstrateSet)){
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155 D835letters<-SecondSubstrateSet[i,4:18]
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156 D835letters<-D835letters[D835letters !="XXXXX"]
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157 D835letters<-paste(D835letters, sep="", collapse="")
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158 leftspaces<-c()
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159 rightspaces<-c()
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160
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161 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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162 YYYposition <- match(x = "x", table = YYYmotif)
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163 #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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164 #just 3 letters to the left of x
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165
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166 YYYLettersToTheLeft <- YYYposition - 1
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167 #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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168 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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169 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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170 #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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171 #variable the user puts in is
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172 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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173 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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174 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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175 #add blank spaces if the motif has less than 4 letters to the left/right
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176 motif<-c(leftspaces,YYYmotif,rightspaces)
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177 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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178 motif<-motif[!motif %in% "x"]
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179 motif<-paste(motif, sep="", collapse="")
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180 D835letters<-motif
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181 D835Ymotifs[i,1]<-D835letters
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182 # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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183 }
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184
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185 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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186 motif<-YYYmotif
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187 #add blank spaces if the motif has less than 4 letters to the left/right
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188 motif<-c(leftspaces,YYYmotif,rightspaces)
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189 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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190 motif<-motif[!motif %in% "x"]
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191 motif<-paste(motif, sep="", collapse="")
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192 D835letters<-motif
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193 D835Ymotifs[i,1]<-D835letters
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194 # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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195 }
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196 }
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197
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198
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199 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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200 ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
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201
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202 for (i in 1:nrow(ThirdSubstrateSet)){
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203 ITDletters<-ThirdSubstrateSet[i,4:18]
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204 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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205 ITDletters<-paste(ITDletters, sep="", collapse="")
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206 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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207 leftspaces<-c()
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208 rightspaces<-c()
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209 YYYposition <- match(x = "x", table = YYYmotif)
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210 #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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211 #just 3 letters to the left of x
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212
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213 YYYLettersToTheLeft <- YYYposition - 1
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214 #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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215 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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216 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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217 #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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218 #variable the user puts in is
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219 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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220 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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221 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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222 #add blank spaces if the motif has less than 4 letters to the left/right
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223 motif<-c(leftspaces,YYYmotif,rightspaces)
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224 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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225 motif<-motif[!motif %in% "x"]
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226 motif<-paste(motif, sep="", collapse="")
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227 ITDletters<-motif
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228 ITDmotifs[i,1]<-ITDletters
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229 # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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230 }
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231
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232 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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233 motif<-YYYmotif
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234 #add blank spaces if the motif has less than 4 letters to the left/right
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235 motif<-c(leftspaces,YYYmotif,rightspaces)
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236 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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237 motif<-motif[!motif %in% "x"]
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238 motif<-paste(motif, sep="", collapse="")
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239 ITDletters<-motif
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240 ITDmotifs[i,1]<-ITDletters
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241 # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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242 }
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243 }
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244
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245 #############################################################################################################################
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246 #############################################################################################################################
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247 #############################################################################################################################
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248 #############################################################################################################################
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249 #############################################################################################################################
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250
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251 #now look for either commonality or difference. Actually could you look for both...
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252
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253 if (Are_You_Looking_For_Commonality=="YES"){
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254
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255 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
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256 columnalheader<-matrix(columnalheader,nrow = 1)
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257
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258 SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
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259 SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
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260
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261
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262 columnalheader<-c(rep(NA,36))
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263 FinalMatrix<-matrix(data =columnalheader,ncol = 1)
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264
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265 SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
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266 AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
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267 AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
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268 AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
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269
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270 for (x in 1:length(AccessionOverlapFinal)) {
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271 for (y in 1:ncol(Firstsubbackfreq)) {
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272 Acc<-AccessionOverlapFinal[x]
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273 SBF<-Firstsubbackfreq[1,y]
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274 if(Acc==SBF){
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275 FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
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276 }
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277 }
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278 }
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279 FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
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280
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281 if(grepl(pattern = "Properties", x=FinalMatrix[22,1])==FALSE){
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282 Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
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283 write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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284 } else {
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285 write.table(x=FinalMatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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286 }
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287
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288 SubstrateMatrix<-SubstrateHeader
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289 if(ncol(SubstrateMatrix)>18){
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290 SubstrateMatrix<-SubstrateMatrix[,1:18]
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291 }
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292
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293 for (z in 1:length(SubstrateOverlapFINAL)) {
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294 motif<-SubstrateOverlapFINAL[z]
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295 newmotif<-unlist(strsplit(motif,split = ""))
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296
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297 Addition<-""
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298 outputmotif<-c(Addition,Addition,Addition,newmotif)
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299 SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
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300 }
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301 write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
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302 }
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