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1 FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE)
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2 Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
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3
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4 SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE)
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5 Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
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6
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7 ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE)
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8 Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
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9
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10
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11 args = commandArgs(trailingOnly=TRUE)
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12
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13 print(args[1])
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14 print(args[2])
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15 print(args[3])
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16
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17
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18 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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19 FullMotifsOnly_questionmark<-args[1]
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20 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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21 TruncatedMotifsOnly_questionmark<-args[2]
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22 #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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23 Are_You_Looking_For_Commonality<-args[3]
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24
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25
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26 #then put the names of your output files here
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27 Shared_motifs_table<-"sharedmotifs.csv"
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28 Shared_subbackfreq_table<-"sharedSBF.csv"
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29
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30 # Shared_motifs_table<-"Shared motifs 7-27-17.csv"
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31 # Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
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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 #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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43 #other languages to see if any of them can do it.
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44 ####################################################################################################################################
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45
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46
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47
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48
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49
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50 FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
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51 FirstSubstrateSet[,11]<-FirstxY
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52
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53 SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
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54 SecondSubstrateSet[,11]<-SecondxY
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55
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56 ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
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57 ThirdSubstrateSet[,11]<-ThirdxY
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58
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59
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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
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67
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68
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69 ####################################################################################################################################
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70 ####################################################################################################################################
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71 # 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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72 # separate proteins thus two separate accession numbers?
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73 # 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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74 # 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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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 #Create the motif sets, deciding wether or not you're looking for truncated or full here
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81 #full only
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82 if (Are_You_Looking_For_Commonality=="YES"){
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83 if (FullMotifsOnly_questionmark=="YES"){
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84 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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85 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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86 leftspaces<-c()
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87 rightspaces<-c()
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88 for (i in 1:nrow(FirstSubstrateSet)){
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89 FTLwtletters<-FirstSubstrateSet[i,4:18]
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90 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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91 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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92
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93
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94 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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95 YYYposition <- match(x = "x", table = YYYmotif)
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96 #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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97 #just 3 letters to the left of x
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98
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99 YYYLettersToTheLeft <- YYYposition - 1
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100 #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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101 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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102 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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103 #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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104 #variable the user puts in is
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105
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106 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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107 motif<-YYYmotif
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108 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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109 motif<-motif[!motif %in% "x"]
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110 motif<-paste(motif, sep="", collapse="")
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111 FTLwtletters<-motif
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112 FTLwtmotifs[i,1]<-FTLwtletters
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113 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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114
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115 }
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116
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117 }
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118 # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
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119 # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
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120 #
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121
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122 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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123 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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124
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125 for (i in 1:nrow(SecondSubstrateSet)){
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126 D835letters<-SecondSubstrateSet[i,4:18]
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127 D835letters<-D835letters[D835letters !="XXXXX"]
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128 D835letters<-paste(D835letters, sep="", collapse="")
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129
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130
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131 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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132 YYYposition <- match(x = "x", table = YYYmotif)
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133 #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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134 #just 3 letters to the left of x
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135
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136 YYYLettersToTheLeft <- YYYposition - 1
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137 #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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138 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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139 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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140 #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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141 #variable the user puts in is
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142
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143 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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144 motif<-YYYmotif
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145 #add blank spaces if the motif has less than 4 letters to the left/right
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146 motif<-c(leftspaces,YYYmotif,rightspaces)
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147 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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148 motif<-motif[!motif %in% "x"]
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149 motif<-paste(motif, sep="", collapse="")
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150 D835letters<-motif
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151 D835Ymotifs[i,1]<-D835letters
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152 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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153
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154 }
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155 }
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156
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157 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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158 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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159
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160 for (i in 1:nrow(ThirdSubstrateSet)){
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161 ITDletters<-ThirdSubstrateSet[i,4:18]
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162 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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163 ITDletters<-paste(ITDletters, sep="", collapse="")
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164 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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165 YYYposition <- match(x = "x", table = YYYmotif)
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166 #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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167 #just 3 letters to the left of x
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168
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169 YYYLettersToTheLeft <- YYYposition - 1
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170 #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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171 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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172 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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173 #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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174 #variable the user puts in is
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175
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176 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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177 motif<-YYYmotif
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178 #add blank spaces if the motif has less than 4 letters to the left/right
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179 motif<-c(leftspaces,YYYmotif,rightspaces)
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180 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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181 motif<-motif[!motif %in% "x"]
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182 motif<-paste(motif, sep="", collapse="")
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183 ITDletters<-motif
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184 ITDmotifs[i,1]<-ITDletters
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185 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
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186
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187 }
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188 }
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189
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190 }
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191
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192 ##############################################3
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193 #Truncated only
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194 if (TruncatedMotifsOnly_questionmark=="YES"){
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195 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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196 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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197
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198 for (i in 1:nrow(FirstSubstrateSet)){
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199 FTLwtletters<-FirstSubstrateSet[i,4:18]
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200 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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201 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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202
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203
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204 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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205 YYYposition <- match(x = "x", table = YYYmotif)
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206 #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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207 #just 3 letters to the left of x
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208
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209 YYYLettersToTheLeft <- YYYposition - 1
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210 #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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211 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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212 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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213 #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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214 #variable the user puts in is
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215
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216 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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217 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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218 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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219 #add blank spaces if the motif has less than 4 letters to the left/right
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220 motif<-c(leftspaces,YYYmotif,rightspaces)
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221 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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222 motif<-motif[!motif %in% "x"]
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223 motif<-paste(motif, sep="", collapse="")
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224 FTLwtletters<-motif
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225 FTLwtmotifs[i,1]<-FTLwtletters
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226 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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227 }
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228
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229 }
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230
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231 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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232 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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233
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234 for (i in 1:nrow(SecondSubstrateSet)){
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235 D835letters<-SecondSubstrateSet[i,4:18]
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236 D835letters<-D835letters[D835letters !="XXXXX"]
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237 D835letters<-paste(D835letters, sep="", collapse="")
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238
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239
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240 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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241 YYYposition <- match(x = "x", table = YYYmotif)
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242 #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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243 #just 3 letters to the left of x
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244
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245 YYYLettersToTheLeft <- YYYposition - 1
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246 #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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247 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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248 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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249 #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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250 #variable the user puts in is
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251
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252 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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253 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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254 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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255 #add blank spaces if the motif has less than 4 letters to the left/right
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256 motif<-c(leftspaces,YYYmotif,rightspaces)
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257 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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258 motif<-motif[!motif %in% "x"]
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259 motif<-paste(motif, sep="", collapse="")
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260 D835letters<-motif
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261 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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262 D835Ymotifs[i,1]<-D835letters
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263 }
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264 }
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265
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266 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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267 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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268
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269 for (i in 1:nrow(ThirdSubstrateSet)){
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270 ITDletters<-ThirdSubstrateSet[i,4:18]
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271 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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272 ITDletters<-paste(ITDletters, sep="", collapse="")
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273 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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274 YYYposition <- match(x = "x", table = YYYmotif)
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275 #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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276 #just 3 letters to the left of x
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277
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278 YYYLettersToTheLeft <- YYYposition - 1
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279 #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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280 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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281 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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282 #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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283 #variable the user puts in is
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284
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285 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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286 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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287 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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288 #add blank spaces if the motif has less than 4 letters to the left/right
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289 motif<-c(leftspaces,YYYmotif,rightspaces)
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290 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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291 motif<-motif[!motif %in% "x"]
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292 motif<-paste(motif, sep="", collapse="")
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293 ITDletters<-motif
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294 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
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295 ITDmotifs[i,1]<-ITDletters
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296 }
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297 }
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298
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299 }
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300
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301 ###############################################
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302 #ALL motifs, full and truncated
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303
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304 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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305 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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306 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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307
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308 for (i in 1:nrow(FirstSubstrateSet)){
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309 FTLwtletters<-FirstSubstrateSet[i,4:18]
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310 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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311 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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312 leftspaces<-c()
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313 rightspaces<-c()
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314
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315 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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316 YYYposition <- match(x = "x", table = YYYmotif)
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317 #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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318 #just 3 letters to the left of x
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319
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320 YYYLettersToTheLeft <- YYYposition - 1
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321 #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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322 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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323 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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324 #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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325 #variable the user puts in is
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326
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327
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328 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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329 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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330 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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331 #add blank spaces if the motif has less than 4 letters to the left/right
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332 motif<-c(leftspaces,YYYmotif,rightspaces)
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333 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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334 motif<-motif[!motif %in% "x"]
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335 motif<-paste(motif, sep="", collapse="")
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336 FTLwtletters<-motif
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337 FTLwtmotifs[i,1]<-FTLwtletters
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338 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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339 }
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340
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341 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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342 motif<-YYYmotif
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343 #add blank spaces if the motif has less than 4 letters to the left/right
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344 motif<-c(leftspaces,YYYmotif,rightspaces)
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345 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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346 motif<-motif[!motif %in% "x"]
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347 motif<-paste(motif, sep="", collapse="")
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348 FTLwtletters<-motif
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349 FTLwtmotifs[i,1]<-FTLwtletters
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350 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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351
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352
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353 }
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354
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355 }
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356
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357 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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358 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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359
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360 for (i in 1:nrow(SecondSubstrateSet)){
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361 D835letters<-SecondSubstrateSet[i,4:18]
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362 D835letters<-D835letters[D835letters !="XXXXX"]
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363 D835letters<-paste(D835letters, sep="", collapse="")
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364 leftspaces<-c()
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365 rightspaces<-c()
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366
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367 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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368 YYYposition <- match(x = "x", table = YYYmotif)
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369 #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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370 #just 3 letters to the left of x
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371
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372 YYYLettersToTheLeft <- YYYposition - 1
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373 #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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374 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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375 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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376 #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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377 #variable the user puts in is
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378 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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379 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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380 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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381 #add blank spaces if the motif has less than 4 letters to the left/right
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382 motif<-c(leftspaces,YYYmotif,rightspaces)
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383 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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384 motif<-motif[!motif %in% "x"]
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385 motif<-paste(motif, sep="", collapse="")
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386 D835letters<-motif
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387 D835Ymotifs[i,1]<-D835letters
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388 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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|
|
389 }
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390
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391 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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392 motif<-YYYmotif
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393 #add blank spaces if the motif has less than 4 letters to the left/right
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394 motif<-c(leftspaces,YYYmotif,rightspaces)
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395 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
396 motif<-motif[!motif %in% "x"]
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|
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397 motif<-paste(motif, sep="", collapse="")
|
|
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398 D835letters<-motif
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|
|
399 D835Ymotifs[i,1]<-D835letters
|
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|
400 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
401 }
|
|
|
402 }
|
|
|
403
|
|
|
404
|
|
|
405 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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|
|
406 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
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407
|
|
|
408 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
409 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
410 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
411 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
412 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
413 leftspaces<-c()
|
|
|
414 rightspaces<-c()
|
|
|
415 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
416 #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
|
|
|
417 #just 3 letters to the left of x
|
|
|
418
|
|
|
419 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
420 #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
|
|
|
421 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
422 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
423 #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
|
|
|
424 #variable the user puts in is
|
|
|
425 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
426 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
427 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
428 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
429 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
430 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
431 motif<-motif[!motif %in% "x"]
|
|
|
432 motif<-paste(motif, sep="", collapse="")
|
|
|
433 ITDletters<-motif
|
|
|
434 ITDmotifs[i,1]<-ITDletters
|
|
|
435 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
436 }
|
|
|
437
|
|
|
438 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
439 motif<-YYYmotif
|
|
|
440 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
441 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
442 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
443 motif<-motif[!motif %in% "x"]
|
|
|
444 motif<-paste(motif, sep="", collapse="")
|
|
|
445 ITDletters<-motif
|
|
|
446 ITDmotifs[i,1]<-ITDletters
|
|
|
447 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
448 }
|
|
|
449 }
|
|
|
450
|
|
|
451 }
|
|
|
452 #############################################################################################################################
|
|
|
453 #############################################################################################################################
|
|
|
454 #############################################################################################################################
|
|
|
455 #############################################################################################################################
|
|
|
456 #############################################################################################################################
|
|
|
457
|
|
|
458 #now look for either commonality or difference. Actually could you look for both...
|
|
|
459
|
|
|
460 if (Are_You_Looking_For_Commonality=="YES"){
|
|
|
461
|
|
|
462 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
463 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
464 # write.table(x=columnalheader,
|
|
|
465 # file=Shared_subbackfreq_table,
|
|
|
466 # quote=FALSE, sep=",",
|
|
|
467 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
468
|
|
|
469 FirstOverlapmotifs<-c()
|
|
|
470 for (i in 1:nrow(ITDmotifs)){
|
|
|
471 for (j in 1:nrow(D835Ymotifs)){
|
|
|
472 if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
|
|
|
473 if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
|
|
|
474 FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
|
|
|
475 }
|
|
|
476 }
|
|
|
477 }
|
|
|
478 }
|
|
|
479
|
|
|
480 AllAccessionNumbers<-c()
|
|
|
481 columnalheader<-c(rep(NA,36))
|
|
|
482 FinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
483
|
|
|
484 FinalMotifs<-c(rep(NA,20))
|
|
|
485 FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
|
|
|
486
|
|
|
487
|
|
|
488 for (l in 1:length(FirstOverlapmotifs)) {
|
|
|
489 AccessionNumber<-00000000000
|
|
|
490 for (k in 1:nrow(FTLwtmotifs)) {
|
|
|
491 AccessionNumber<-0000000000000
|
|
|
492 if(is.na(FTLwtmotifs[k])!=TRUE){
|
|
|
493 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
494 #destroyed immediately after use
|
|
|
495 if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
|
|
|
496 substratematrix<-FirstSubstrateSet[k,1:20]
|
|
|
497 substratematrix<-as.matrix(substratematrix,nrow=1)
|
|
|
498 FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
|
|
|
499 #when you find a match between the venn diagrams, save the substrate info you get into a matrix
|
|
|
500
|
|
|
501 AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
|
|
|
502 #then take the accession number
|
|
|
503
|
|
|
504 for (m in 1:ncol(Firstsubbackfreq)) {
|
|
|
505 AN <- as.character(Firstsubbackfreq[1, m])
|
|
|
506 if (grepl(pattern = AN,
|
|
|
507 x = AccessionNumber,
|
|
|
508 fixed = TRUE) == TRUE) {
|
|
|
509 outputmatrix <- as.character(Firstsubbackfreq[, m])
|
|
|
510 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
511 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
512 FinalMatrix<-rbind(FinalMatrix,outputmatrix)
|
|
|
513 }
|
|
|
514 }
|
|
|
515 }
|
|
|
516 }
|
|
|
517 }
|
|
|
518 }
|
|
|
519
|
|
|
520
|
|
|
521 TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
|
|
|
522 TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
|
|
|
523
|
|
|
524 TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
|
|
|
525 TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
|
|
|
526
|
|
|
527 write.table(
|
|
|
528 x = TrueFinalMotifsMatrix,
|
|
|
529 file = Shared_motifs_table,
|
|
|
530 quote = FALSE,
|
|
|
531 sep = ",",
|
|
|
532 row.names = FALSE,
|
|
|
533 col.names = TRUE,
|
|
|
534 na = "",
|
|
|
535 append = FALSE
|
|
|
536 )
|
|
|
537
|
|
|
538 #TrueMatrix<-t(TrueMatrix)
|
|
|
539 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
540 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
541
|
|
|
542 TrueMatrix<-rbind(columnalheader,TrueMatrix)
|
|
|
543 TrueMatrix<-t(TrueMatrix)
|
|
|
544
|
|
|
545 write.table(
|
|
|
546 x = TrueMatrix,
|
|
|
547 file = Shared_subbackfreq_table,
|
|
|
548 quote = FALSE,
|
|
|
549 sep = ",",
|
|
|
550 row.names = FALSE,
|
|
|
551 col.names = FALSE,
|
|
|
552 na = "",
|
|
|
553 append = TRUE
|
|
|
554 )
|
|
|
555 }
|
|
|
556 }
|
|
|
557
|
|
|
558 if (Are_You_Looking_For_Commonality=="NO"){
|
|
|
559 if (FullMotifsOnly_questionmark=="YES"){
|
|
|
560 FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
561 FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
562 leftspaces<-c()
|
|
|
563 rightspaces<-c()
|
|
|
564 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
565 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
566 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
567 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
568
|
|
|
569
|
|
|
570 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
571 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
572 #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
|
|
|
573 #just 3 letters to the left of x
|
|
|
574
|
|
|
575 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
576 #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
|
|
|
577 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
578 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
579 #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
|
|
|
580 #variable the user puts in is
|
|
|
581
|
|
|
582 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
583 motif<-YYYmotif
|
|
|
584 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
585 motif<-motif[!motif %in% "x"]
|
|
|
586 motif<-paste(motif, sep="", collapse="")
|
|
|
587 FTLwtletters<-motif
|
|
|
588 FTLwtmotifs[i]<-FTLwtletters
|
|
|
589 FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
|
|
|
590 }
|
|
|
591
|
|
|
592 }
|
|
|
593 # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
|
|
|
594 # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
|
|
|
595 #
|
|
|
596
|
|
|
597 D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
598 D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
599
|
|
|
600 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
601 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
602 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
603 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
604
|
|
|
605
|
|
|
606 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
607 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
608 #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
|
|
|
609 #just 3 letters to the left of x
|
|
|
610
|
|
|
611 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
612 #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
|
|
|
613 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
614 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
615 #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
|
|
|
616 #variable the user puts in is
|
|
|
617
|
|
|
618 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
619 motif<-YYYmotif
|
|
|
620 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
621 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
622 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
623 motif<-motif[!motif %in% "x"]
|
|
|
624 motif<-paste(motif, sep="", collapse="")
|
|
|
625 D835letters<-motif
|
|
|
626 D835Ymotifs[i]<-D835letters
|
|
|
627 D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
|
|
|
628 }
|
|
|
629 }
|
|
|
630
|
|
|
631 ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
632 ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
633
|
|
|
634 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
635 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
636 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
637 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
638 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
639 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
640 #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
|
|
|
641 #just 3 letters to the left of x
|
|
|
642
|
|
|
643 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
644 #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
|
|
|
645 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
646 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
647 #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
|
|
|
648 #variable the user puts in is
|
|
|
649
|
|
|
650 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
651 motif<-YYYmotif
|
|
|
652 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
653 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
654 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
655 motif<-motif[!motif %in% "x"]
|
|
|
656 motif<-paste(motif, sep="", collapse="")
|
|
|
657 ITDletters<-motif
|
|
|
658 ITDmotifs[i]<-ITDletters
|
|
|
659 ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
|
|
|
660
|
|
|
661 }
|
|
|
662 }
|
|
|
663 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
664 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
665 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
666 }
|
|
|
667
|
|
|
668
|
|
|
669 ##############################################3
|
|
|
670 #Truncated only
|
|
|
671 if (TruncatedMotifsOnly_questionmark=="YES"){
|
|
|
672 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
673 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
674
|
|
|
675 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
676 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
677 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
678 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
679
|
|
|
680
|
|
|
681 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
682 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
683 #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
|
|
|
684 #just 3 letters to the left of x
|
|
|
685
|
|
|
686 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
687 #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
|
|
|
688 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
689 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
690 #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
|
|
|
691 #variable the user puts in is
|
|
|
692
|
|
|
693 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
694 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
695 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
696 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
697 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
698 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
699 motif<-motif[!motif %in% "x"]
|
|
|
700 motif<-paste(motif, sep="", collapse="")
|
|
|
701 FTLwtletters<-motif
|
|
|
702 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
703 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
704 }
|
|
|
705
|
|
|
706 }
|
|
|
707
|
|
|
708 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
|
|
|
709 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
|
|
|
710 i=2
|
|
|
711 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
712 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
713 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
714 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
715
|
|
|
716
|
|
|
717 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
718 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
719 #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
|
|
|
720 #just 3 letters to the left of x
|
|
|
721
|
|
|
722 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
723 #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
|
|
|
724 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
725 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
726 #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
|
|
|
727 #variable the user puts in is
|
|
|
728
|
|
|
729 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
730 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
731 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
732 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
733 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
734 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
735 motif<-motif[!motif %in% "x"]
|
|
|
736 motif<-paste(motif, sep="", collapse="")
|
|
|
737 D835letters<-motif
|
|
|
738 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
|
|
|
739 D835Ymotifs[i,1]<-D835letters
|
|
|
740 }
|
|
|
741 }
|
|
|
742
|
|
|
743 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
|
|
|
744 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
|
745
|
|
|
746 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
747 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
748 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
749 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
750 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
751 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
752 #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
|
|
|
753 #just 3 letters to the left of x
|
|
|
754
|
|
|
755 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
756 #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
|
|
|
757 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
758 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
759 #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
|
|
|
760 #variable the user puts in is
|
|
|
761
|
|
|
762 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
763 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
764 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
765 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
766 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
767 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
768 motif<-motif[!motif %in% "x"]
|
|
|
769 motif<-paste(motif, sep="", collapse="")
|
|
|
770 ITDletters<-motif
|
|
|
771 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
|
|
|
772 ITDmotifs[i,1]<-ITDletters
|
|
|
773 }
|
|
|
774 }
|
|
|
775 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
776 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
777 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
778 }
|
|
|
779
|
|
|
780 ###############################################
|
|
|
781 #ALL motifs, full and truncated
|
|
|
782
|
|
|
783 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
|
|
|
784 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
785 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
786
|
|
|
787 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
788 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
789 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
790 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
791 leftspaces<-c()
|
|
|
792 rightspaces<-c()
|
|
|
793
|
|
|
794 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
795 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
796 #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
|
|
|
797 #just 3 letters to the left of x
|
|
|
798
|
|
|
799 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
800 #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
|
|
|
801 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
802 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
803 #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
|
|
|
804 #variable the user puts in is
|
|
|
805
|
|
|
806
|
|
|
807 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
808 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
809 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
810 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
811 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
812 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
813 motif<-motif[!motif %in% "x"]
|
|
|
814 motif<-paste(motif, sep="", collapse="")
|
|
|
815 FTLwtletters<-motif
|
|
|
816 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
817 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
818 }
|
|
|
819
|
|
|
820 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
821 motif<-YYYmotif
|
|
|
822 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
823 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
824 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
825 motif<-motif[!motif %in% "x"]
|
|
|
826 motif<-paste(motif, sep="", collapse="")
|
|
|
827 FTLwtletters<-motif
|
|
|
828 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
829 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
830
|
|
|
831
|
|
|
832 }
|
|
|
833
|
|
|
834 }
|
|
|
835
|
|
|
836 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
|
|
|
837 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
|
|
|
838
|
|
|
839 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
840 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
841 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
842 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
843 leftspaces<-c()
|
|
|
844 rightspaces<-c()
|
|
|
845
|
|
|
846 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
847 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
848 #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
|
|
|
849 #just 3 letters to the left of x
|
|
|
850
|
|
|
851 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
852 #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
|
|
|
853 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
854 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
855 #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
|
|
|
856 #variable the user puts in is
|
|
|
857 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
858 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
859 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
860 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
861 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
862 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
863 motif<-motif[!motif %in% "x"]
|
|
|
864 motif<-paste(motif, sep="", collapse="")
|
|
|
865 D835letters<-motif
|
|
|
866 D835Ymotifs[i,1]<-D835letters
|
|
|
867 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
868 }
|
|
|
869
|
|
|
870 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
871 motif<-YYYmotif
|
|
|
872 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
873 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
874 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
875 motif<-motif[!motif %in% "x"]
|
|
|
876 motif<-paste(motif, sep="", collapse="")
|
|
|
877 D835letters<-motif
|
|
|
878 D835Ymotifs[i,1]<-D835letters
|
|
|
879 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
880 }
|
|
|
881 }
|
|
|
882
|
|
|
883
|
|
|
884 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
|
|
|
885 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
|
886
|
|
|
887 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
888 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
889 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
890 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
891 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
892 leftspaces<-c()
|
|
|
893 rightspaces<-c()
|
|
|
894 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
895 #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
|
|
|
896 #just 3 letters to the left of x
|
|
|
897
|
|
|
898 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
899 #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
|
|
|
900 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
901 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
902 #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
|
|
|
903 #variable the user puts in is
|
|
|
904 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
905 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
906 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
907 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
908 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
909 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
910 motif<-motif[!motif %in% "x"]
|
|
|
911 motif<-paste(motif, sep="", collapse="")
|
|
|
912 ITDletters<-motif
|
|
|
913 ITDmotifs[i,1]<-ITDletters
|
|
|
914 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
915 }
|
|
|
916
|
|
|
917 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
918 motif<-YYYmotif
|
|
|
919 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
920 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
921 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
922 motif<-motif[!motif %in% "x"]
|
|
|
923 motif<-paste(motif, sep="", collapse="")
|
|
|
924 ITDletters<-motif
|
|
|
925 ITDmotifs[i,1]<-ITDletters
|
|
|
926 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
927 }
|
|
|
928 }
|
|
|
929 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
930 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
931 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
932 }
|
|
|
933
|
|
|
934
|
|
|
935 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
|
|
|
936 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
|
|
|
937 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
|
|
|
938
|
|
|
939
|
|
|
940 ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
|
|
|
941 ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
|
|
|
942 ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
|
|
|
943
|
|
|
944
|
|
|
945 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
|
|
|
946 D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
|
|
|
947 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
|
|
|
948
|
|
|
949
|
|
|
950 columnalheader<-c(rep(NA,36))
|
|
|
951 FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
952
|
|
|
953 for (k in 1:length(FTLwtmotifsFINAL)) {
|
|
|
954 AN<-00000
|
|
|
955 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
956 #destroyed immediately after use
|
|
|
957 for (m in 1:ncol(Firstsubbackfreq)) {
|
|
|
958 AN <- as.character(Firstsubbackfreq[1, m])
|
|
|
959 if (grepl(pattern = AN,
|
|
|
960 x = names(FTLwtmotifsFINAL[k]),
|
|
|
961 fixed = TRUE) == TRUE) {
|
|
|
962 outputmatrix <- as.character(Firstsubbackfreq[, m])
|
|
|
963 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
964 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
965 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
|
|
|
966 }
|
|
|
967 }
|
|
|
968 }
|
|
|
969 FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
|
|
|
970
|
|
|
971 columnalheader<-c(rep(NA,36))
|
|
|
972 ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
973
|
|
|
974 for (k in 1:length(ITDmotifsFINAL)) {
|
|
|
975 AN<-00000
|
|
|
976 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
977 #destroyed immediately after use
|
|
|
978 for (m in 1:ncol(Thirdsubbackfreq)) {
|
|
|
979 AN <- as.character(Thirdsubbackfreq[1, m])
|
|
|
980 if (grepl(pattern = AN,
|
|
|
981 x = names(ITDmotifsFINAL[k]),
|
|
|
982 fixed = TRUE) == TRUE) {
|
|
|
983 outputmatrix <- as.character(Thirdsubbackfreq[, m])
|
|
|
984 outputmatrix <- matrix(outputmatrix, nrow = 1)
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|
|
985 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
986 ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
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|
|
987 }
|
|
|
988 }
|
|
|
989 }
|
|
|
990 ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
|
|
|
991
|
|
|
992 columnalheader<-c(rep(NA,36))
|
|
|
993 D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
994
|
|
|
995 for (k in 1:length(D835YmotifsFINAL)) {
|
|
|
996 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
997 #destroyed immediately after use
|
|
|
998 for (m in 1:ncol(Secondsubbackfreq)) {
|
|
|
999 AN <- as.character(Secondsubbackfreq[1, m])
|
|
|
1000 if (grepl(pattern = AN,
|
|
|
1001 x = names(D835YmotifsFINAL[k]),
|
|
|
1002 fixed = TRUE) == TRUE) {
|
|
|
1003 outputmatrix <- as.character(Secondsubbackfreq[, m])
|
|
|
1004 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
1005 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
1006 D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
|
|
|
1007 }
|
|
|
1008 }
|
|
|
1009 }
|
|
|
1010 D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
|
|
|
1011
|
|
|
1012 FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
|
|
|
1013
|
|
|
1014 #another fucking for loop
|
|
|
1015 FLTreference<-FTLoutputmatrix[,2]
|
|
|
1016
|
|
|
1017 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1018 FirstLine<-FirstLine[1:23]
|
|
|
1019 for (q in 1:nrow(FTLoutputmatrix)) {
|
|
|
1020 thismotif<-unlist(strsplit(FTLoutputmatrix[q,1],""))
|
|
|
1021 thisoutput<-c("","",FTLoutputmatrix[q,2],thismotif,"","","","","")
|
|
|
1022 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1023 }
|
|
|
1024
|
|
|
1025
|
|
|
1026
|
|
|
1027 write.table(x=FirstLine,
|
|
|
1028 file=First_unshared_motifs_table,
|
|
|
1029 quote=FALSE, sep=",",
|
|
|
1030 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1031
|
|
|
1032 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1033 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1034
|
|
|
1035 # columnalheader<-rbind(columnalheader,FTLFinalMatrix)
|
|
|
1036
|
|
|
1037 write.table(x=columnalheader,
|
|
|
1038 file=First_unshared_subbackfreq,
|
|
|
1039 quote=FALSE, sep=",",
|
|
|
1040 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1041
|
|
|
1042 write.table(x=FTLFinalMatrix[2:nrow(FTLFinalMatrix),],
|
|
|
1043 file=First_unshared_subbackfreq,
|
|
|
1044 quote=FALSE, sep=",",
|
|
|
1045 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1046
|
|
|
1047 ############################################################################################################
|
|
|
1048
|
|
|
1049 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
|
|
|
1050
|
|
|
1051 FLTreference<-D835Youtputmatrix[,2]
|
|
|
1052
|
|
|
1053 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1054 FirstLine<-FirstLine[1:23]
|
|
|
1055 for (q in 1:nrow(D835Youtputmatrix)) {
|
|
|
1056 thismotif<-unlist(strsplit(D835Youtputmatrix[q,1],""))
|
|
|
1057 thisoutput<-c("","",D835Youtputmatrix[q,2],thismotif,"","","","","")
|
|
|
1058 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1059 }
|
|
|
1060
|
|
|
1061
|
|
|
1062
|
|
|
1063 write.table(x=FirstLine,
|
|
|
1064 file=Second_unshared_motifs_table,
|
|
|
1065 quote=FALSE, sep=",",
|
|
|
1066 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1067
|
|
|
1068 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1069 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1070
|
|
|
1071 # columnalheader<-rbind(columnalheader,D835YFinalMatrix)
|
|
|
1072
|
|
|
1073 write.table(x=columnalheader,
|
|
|
1074 file=Second_unshared_subbackfreq,
|
|
|
1075 quote=FALSE, sep=",",
|
|
|
1076 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1077
|
|
|
1078 write.table(x=D835YFinalMatrix[2:nrow(D835YFinalMatrix),],
|
|
|
1079 file=Second_unshared_subbackfreq,
|
|
|
1080 quote=FALSE, sep=",",
|
|
|
1081 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1082
|
|
|
1083 ############################################################################################################
|
|
|
1084
|
|
|
1085 ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
|
|
|
1086
|
|
|
1087 FLTreference<-ITDoutputmatrix[,2]
|
|
|
1088
|
|
|
1089 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1090 FirstLine<-FirstLine[1:23]
|
|
|
1091 for (q in 1:nrow(ITDoutputmatrix)) {
|
|
|
1092 thismotif<-unlist(strsplit(ITDoutputmatrix[q,1],""))
|
|
|
1093 thisoutput<-c("","",ITDoutputmatrix[q,2],thismotif,"","","","","")
|
|
|
1094 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1095 }
|
|
|
1096
|
|
|
1097
|
|
|
1098 write.table(x=FirstLine,
|
|
|
1099 file=Third_unshared_motifs_table,
|
|
|
1100 quote=FALSE, sep=",",
|
|
|
1101 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1102
|
|
|
1103 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1104 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1105
|
|
|
1106 # columnalheader<-rbind(columnalheader,ITDFinalMatrix)
|
|
|
1107
|
|
|
1108 write.table(x=columnalheader,
|
|
|
1109 file=Third_unshared_subbackfreq,
|
|
|
1110 quote=FALSE, sep=",",
|
|
|
1111 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1112
|
|
|
1113 write.table(x=ITDFinalMatrix[2:nrow(ITDFinalMatrix),],
|
|
|
1114 file=Third_unshared_subbackfreq,
|
|
|
1115 quote=FALSE, sep=",",
|
|
|
1116 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1117
|
|
|
1118 }
|
