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4
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1 #I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon
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2 #the output files have both Y and xY, they shouldn't why is that happening? make it not happen
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3 #make sure that accession numbers stay locked to each motif, somehow
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4 #output should look just like the KALIP input
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5
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6 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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7 FullMotifsOnly_questionmark<-"NO"
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8 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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9 TruncatedMotifsOnly_questionmark<-"NO"
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10 #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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11 Are_You_Looking_For_Commonality<-"NO"
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12
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13
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14 #put the names of your input files here
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15 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
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16 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
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17
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18 SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
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19 Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)
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20
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21 # ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE)
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22 # Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE)
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23
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24 #then put the names of your output files here
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25 # Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv"
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26 # Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv"
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27
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28 # Shared_motifs_table<-"Shared motifs 7-27-17.csv"
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29 # Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
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30
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31 First_unshared_motifs_table<-"1RS.csv"
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32 First_unshared_subbackfreq<-"1RSBF.csv"
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33
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34 Second_unshared_motifs_table<-"2RS.csv"
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35 Second_unshared_subbackfreq<-"2RSBF.csv"
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36
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37 # Third_unshared_motifs_table<-"R3 subs.csv"
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38 # Third_unshared_subbackfreq<-"R3 SBF.csv"
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39
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40 #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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41 #other languages to see if any of them can do it.
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42 ####################################################################################################################################
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43
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44
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45
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46
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47
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48 # grepl(pattern = "S", x=asdf, ignore.case = TRUE)
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49
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50 FirstCentralLetters<-FirstSubstrateSet[,11]
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51 SecondCentralLetters<-SecondSubstrateSet[,11]
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52
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53 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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54 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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55 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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56
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57 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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58 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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59 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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60
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61 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
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62 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
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63 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
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64
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65 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
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66 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
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67 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
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68
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69 FirstCentralLetters->FirstSubstrateSet[,11]
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70 SecondCentralLetters->SecondSubstrateSet[,11]
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71
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72 ####################################################################################################################################
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73 ####################################################################################################################################
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74 # 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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75 # separate proteins thus two separate accession numbers?
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76 # 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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77 # 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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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 #Create the motif sets, deciding wether or not you're looking for truncated or full here
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84 #full only
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85
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86
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87 if (Are_You_Looking_For_Commonality=="NO"){
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88
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89 ###############################################
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90 #ALL motifs, full and truncated
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91
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92 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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93 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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94 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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95
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96 for (i in 1:nrow(FirstSubstrateSet)){
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97 FTLwtletters<-FirstSubstrateSet[i,4:18]
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98 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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99 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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100 leftspaces<-c()
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101 rightspaces<-c()
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102
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103 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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104 YYYposition <- match(x = "x", table = YYYmotif)
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105 #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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106 #just 3 letters to the left of x
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107
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108 YYYLettersToTheLeft <- YYYposition - 1
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109 #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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110 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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111 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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112 #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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113 #variable the user puts in is
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114
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115
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116 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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117 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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118 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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119 #add blank spaces if the motif has less than 4 letters to the left/right
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120 motif<-c(leftspaces,YYYmotif,rightspaces)
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121 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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122 motif<-motif[!motif %in% "x"]
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123 motif<-paste(motif, sep="", collapse="")
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124 FTLwtletters<-motif
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125 FTLwtmotifs[i,1]<-FTLwtletters
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126 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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127 }
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128
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129 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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130 motif<-YYYmotif
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131 #add blank spaces if the motif has less than 4 letters to the left/right
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132 motif<-c(leftspaces,YYYmotif,rightspaces)
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133 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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134 motif<-motif[!motif %in% "x"]
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135 motif<-paste(motif, sep="", collapse="")
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136 FTLwtletters<-motif
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137 FTLwtmotifs[i,1]<-FTLwtletters
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138 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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139
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140
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141 }
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142
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143 }
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144
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145 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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146 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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147
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148 for (i in 1:nrow(SecondSubstrateSet)){
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149 D835letters<-SecondSubstrateSet[i,4:18]
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150 D835letters<-D835letters[D835letters !="XXXXX"]
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151 D835letters<-paste(D835letters, sep="", collapse="")
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152 leftspaces<-c()
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153 rightspaces<-c()
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154
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155 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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156 YYYposition <- match(x = "x", table = YYYmotif)
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157 #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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158 #just 3 letters to the left of x
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159
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160 YYYLettersToTheLeft <- YYYposition - 1
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161 #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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162 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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163 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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164 #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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165 #variable the user puts in is
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166 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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167 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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168 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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169 #add blank spaces if the motif has less than 4 letters to the left/right
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170 motif<-c(leftspaces,YYYmotif,rightspaces)
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171 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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172 motif<-motif[!motif %in% "x"]
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173 motif<-paste(motif, sep="", collapse="")
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174 D835letters<-motif
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175 D835Ymotifs[i,1]<-D835letters
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176 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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177 }
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178
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179 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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180 motif<-YYYmotif
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181 #add blank spaces if the motif has less than 4 letters to the left/right
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182 motif<-c(leftspaces,YYYmotif,rightspaces)
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183 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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184 motif<-motif[!motif %in% "x"]
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185 motif<-paste(motif, sep="", collapse="")
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186 D835letters<-motif
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187 D835Ymotifs[i,1]<-D835letters
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188 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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189 }
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190 }
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191
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192 names(FTLwtmotifs)<-FTLwtAccessionNumbers
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193 names(D835Ymotifs)<-D835YAccessionNumbers
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194
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195 }
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196
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197
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198 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
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199 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
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200
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201 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
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202 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
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203
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204
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205 columnalheader<-c(rep(NA,36))
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206 FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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207
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208 for (k in 1:length(FTLwtmotifsFINAL)) {
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209 AN<-00000
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210 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
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211 #destroyed immediately after use
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212 for (m in 1:ncol(Firstsubbackfreq)) {
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213 AN <- as.character(Firstsubbackfreq[1, m])
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214 if (grepl(pattern = AN,
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215 x = names(FTLwtmotifsFINAL[k]),
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216 fixed = TRUE) == TRUE) {
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217 outputmatrix <- as.character(Firstsubbackfreq[, m])
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218 outputmatrix <- matrix(outputmatrix, nrow = 1)
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219 #with that accession number, find a match in the subbackfreq file and save it here
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220 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
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221 }
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222 }
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223 }
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224 FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
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225 FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
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226
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227 columnalheader<-c(rep(NA,36))
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228 D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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229
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230 for (k in 1:length(D835YmotifsFINAL)) {
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231 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
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232 #destroyed immediately after use
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233 for (m in 1:ncol(Secondsubbackfreq)) {
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234 AN <- as.character(Secondsubbackfreq[1, m])
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235 if (grepl(pattern = AN,
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236 x = names(D835YmotifsFINAL[k]),
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237 fixed = TRUE) == TRUE) {
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238 outputmatrix <- as.character(Secondsubbackfreq[, m])
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239 outputmatrix <- matrix(outputmatrix, nrow = 1)
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240 #with that accession number, find a match in the subbackfreq file and save it here
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241 D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
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242 }
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243 }
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244 }
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245 D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
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246 D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),]
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247
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248 FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
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249
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250
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251 FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
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252 # FLTheader<-unlist(FLTheader)
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253 lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
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254 righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
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255 FLTaccessionset<-FTLoutputmatrix[,2]
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256 FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
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257 FTLmeat<-sapply(FTLmeat, unlist)
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258 colnames(FTLmeat)<-NULL
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259 FTLmeat<-t(FTLmeat)
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260
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261 FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT)
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262 colnames(FTLoutputmatrix2)<-NULL
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263 rownames(FTLoutputmatrix2)<-NULL
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264 colnames(FLTheader)<-NULL
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265 rownames(FLTheader)<-NULL
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266
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267
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268 FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11]
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269
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270 FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
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271 FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
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272 FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
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273
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274 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS")
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275 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT")
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276 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY")
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277
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278 FirstCentralLettersAGAIN->FTLoutputmatrix2[,11]
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279
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280 FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2)
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281
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282 write.table(x=FTLoutputmatrix2,
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283 file=First_unshared_motifs_table,
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284 quote=FALSE, sep=",",
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285 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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286
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287 columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
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288 columnalheader<-matrix(columnalheader,nrow = 1)
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289 write.table(x=columnalheader,
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290 file=First_unshared_subbackfreq,
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291 quote=FALSE, sep=",",
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292 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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293
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294 write.table(x=FTLFinalMatrix,
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295 file=First_unshared_subbackfreq,
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296 quote=FALSE, sep=",",
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297 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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298
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299 ############################################################################################################
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300
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301 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
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302
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303 D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
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304 # D835Yheader<-unlist(D835Yheader)
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305 lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
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306 righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
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307 D835Yaset<-D835Youtputmatrix[,2]
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308 D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "")
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309 D835meat<-sapply(D835meat, unlist)
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310 colnames(D835meat)<-NULL
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311 D835meat<-t(D835meat)
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312
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313 D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835)
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314 colnames(D835Youtputmatrix2)<-NULL
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315 rownames(D835Youtputmatrix2)<-NULL
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316 colnames(D835Yheader)<-NULL
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317 rownames(D835Yheader)<-NULL
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318
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319
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320 SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11]
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321
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322 SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
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323 SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
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324 SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
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325
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326 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS")
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327 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT")
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328 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY")
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329
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330 SecondCentralLettersAGAIN->D835Youtputmatrix2[,11]
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331
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332 D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2)
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333
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334 write.table(x=D835Youtputmatrix2,
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335 file=Second_unshared_motifs_table,
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336 quote=FALSE, sep=",",
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337 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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338
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339 columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1]))
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340 columnalheader<-matrix(columnalheader,nrow = 1)
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341 write.table(x=columnalheader,
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342 file=Second_unshared_subbackfreq,
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343 quote=FALSE, sep=",",
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344 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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345
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346 write.table(x=D835YFinalMatrix,
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347 file=Second_unshared_subbackfreq,
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348 quote=FALSE, sep=",",
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349 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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350 }
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351
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