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1 #########################################################################################
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2 # License Agreement
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3 #
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4 # THIS WORK IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE
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5 # ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER
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6 # APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE
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7 # OR COPYRIGHT LAW IS PROHIBITED.
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8 #
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9 # BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE
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10 # BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED
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11 # TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN
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12 # CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
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13 #
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14 # BASELIne: Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences
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15 # Coded by: Mohamed Uduman & Gur Yaari
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16 # Copyright 2012 Kleinstein Lab
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17 # Version: 1.3 (01/23/2014)
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18 #########################################################################################
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19
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20 op <- options();
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21 options(showWarnCalls=FALSE, showErrorCalls=FALSE, warn=-1)
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22 library('seqinr')
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23 if( F & Sys.info()[1]=="Linux"){
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24 library("multicore")
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25 }
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26
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27 # Load functions and initialize global variables
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28 source("Baseline_Functions.r")
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29
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30 # Initialize parameters with user provided arguments
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31 arg <- commandArgs(TRUE)
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32 #arg = c(2,1,5,5,0,1,"1:26:38:55:65:104:116", "test.fasta","","sample")
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33 #arg = c(1,1,5,5,0,1,"1:38:55:65:104:116:200", "test.fasta","","sample")
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34 #arg = c(1,1,5,5,1,1,"1:26:38:55:65:104:116", "/home/mu37/Wu/Wu_Cloned_gapped_sequences_D-masked.fasta","/home/mu37/Wu/","Wu")
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35 testID <- as.numeric(arg[1]) # 1 = Focused, 2 = Local
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36 species <- as.numeric(arg[2]) # 1 = Human. 2 = Mouse
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37 substitutionModel <- as.numeric(arg[3]) # 0 = Uniform substitution, 1 = Smith DS et al. 1996, 5 = FiveS
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38 mutabilityModel <- as.numeric(arg[4]) # 0 = Uniform mutablity, 1 = Tri-nucleotide (Shapiro GS et al. 2002) , 5 = FiveS
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39 clonal <- as.numeric(arg[5]) # 0 = Independent sequences, 1 = Clonally related, 2 = Clonally related & only non-terminal mutations
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40 fixIndels <- as.numeric(arg[6]) # 0 = Do nothing, 1 = Try and fix Indels
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41 region <- as.numeric(strsplit(arg[7],":")[[1]]) # StartPos:LastNucleotideF1:C1:F2:C2:F3:C3
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42 inputFilePath <- arg[8] # Full path to input file
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43 outputPath <- arg[9] # Full path to location of output files
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44 outputID <- arg[10] # ID for session output
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45
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46
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47 if(testID==5){
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48 traitChangeModel <- 1
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49 if( !is.na(any(arg[11])) ) traitChangeModel <- as.numeric(arg[11]) # 1 <- Chothia 1998
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50 initializeTraitChange(traitChangeModel)
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51 }
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52
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53 # Initialize other parameters/variables
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54
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55 # Initialzie the codon table ( definitions of R/S )
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56 computeCodonTable(testID)
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57
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58 # Initialize
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59 # Test Name
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60 testName<-"Focused"
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61 if(testID==2) testName<-"Local"
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62 if(testID==3) testName<-"Imbalanced"
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63 if(testID==4) testName<-"ImbalancedSilent"
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64
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65 # Indel placeholders initialization
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66 indelPos <- NULL
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67 delPos <- NULL
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68 insPos <- NULL
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69
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70 # Initialize in Tranistion & Mutability matrixes
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71 substitution <- initializeSubstitutionMatrix(substitutionModel,species)
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72 mutability <- initializeMutabilityMatrix(mutabilityModel,species)
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73
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74 # FWR/CDR boundaries
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75 flagTrim <- F
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76 if( is.na(region[7])){
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77 flagTrim <- T
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78 region[7]<-region[6]
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79 }
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80 readStart = min(region,na.rm=T)
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81 readEnd = max(region,na.rm=T)
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82 if(readStart>1){
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83 region = region - (readStart - 1)
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84 }
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85 region_Nuc = c( (region[1]*3-2) , (region[2:7]*3) )
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86 region_Cod = region
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87
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88 readStart = (readStart*3)-2
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89 readEnd = (readEnd*3)
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90
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91 FWR_Nuc <- c( rep(TRUE,(region_Nuc[2])),
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92 rep(FALSE,(region_Nuc[3]-region_Nuc[2])),
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93 rep(TRUE,(region_Nuc[4]-region_Nuc[3])),
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94 rep(FALSE,(region_Nuc[5]-region_Nuc[4])),
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95 rep(TRUE,(region_Nuc[6]-region_Nuc[5])),
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96 rep(FALSE,(region_Nuc[7]-region_Nuc[6]))
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97 )
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98 CDR_Nuc <- (1-FWR_Nuc)
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99 CDR_Nuc <- as.logical(CDR_Nuc)
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100 FWR_Nuc_Mat <- matrix( rep(FWR_Nuc,4), ncol=length(FWR_Nuc), nrow=4, byrow=T)
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101 CDR_Nuc_Mat <- matrix( rep(CDR_Nuc,4), ncol=length(CDR_Nuc), nrow=4, byrow=T)
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102
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103 FWR_Codon <- c( rep(TRUE,(region[2])),
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104 rep(FALSE,(region[3]-region[2])),
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105 rep(TRUE,(region[4]-region[3])),
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106 rep(FALSE,(region[5]-region[4])),
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107 rep(TRUE,(region[6]-region[5])),
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108 rep(FALSE,(region[7]-region[6]))
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109 )
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110 CDR_Codon <- (1-FWR_Codon)
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111 CDR_Codon <- as.logical(CDR_Codon)
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112
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113
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114 # Read input FASTA file
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115 tryCatch(
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116 inputFASTA <- baseline.read.fasta(inputFilePath, seqtype="DNA",as.string=T,set.attributes=F,forceDNAtolower=F)
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117 , error = function(ex){
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118 cat("Error|Error reading input. Please enter or upload a valid FASTA file.\n")
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119 q()
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120 }
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121 )
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122
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123 if (length(inputFASTA)==1) {
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124 cat("Error|Error reading input. Please enter or upload a valid FASTA file.\n")
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125 q()
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126 }
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127
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128 # Process sequence IDs/names
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129 names(inputFASTA) <- sapply(names(inputFASTA),function(x){trim(x)})
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130
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131 # Convert non nucleotide characters to N
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132 inputFASTA[length(inputFASTA)] = gsub("\t","",inputFASTA[length(inputFASTA)])
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133 inputFASTA <- lapply(inputFASTA,replaceNonFASTAChars)
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134
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135 # Process the FASTA file and conver to Matrix[inputSequence, germlineSequence]
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136 processedInput <- processInputAdvanced(inputFASTA)
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137 matInput <- processedInput[[1]]
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138 germlines <- processedInput[[2]]
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139 lenGermlines = length(unique(germlines))
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140 groups <- processedInput[[3]]
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141 lenGroups = length(unique(groups))
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142 rm(processedInput)
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143 rm(inputFASTA)
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144
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145 # # remove clones with less than 2 seqeunces
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146 # tableGL <- table(germlines)
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147 # singletons <- which(tableGL<8)
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148 # rowsToRemove <- match(singletons,germlines)
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149 # if(any(rowsToRemove)){
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150 # matInput <- matInput[-rowsToRemove,]
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151 # germlines <- germlines[-rowsToRemove]
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152 # groups <- groups[-rowsToRemove]
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153 # }
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154 #
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155 # # remove unproductive seqs
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156 # nonFuctionalSeqs <- sapply(rownames(matInput),function(x){any(grep("unproductive",x))})
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157 # if(any(nonFuctionalSeqs)){
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158 # if(sum(nonFuctionalSeqs)==length(germlines)){
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159 # write.table("Unproductive",file=paste(outputPath,outputID,".txt",sep=""),quote=F,sep="\t",row.names=F,col.names=T)
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160 # q()
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161 # }
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162 # matInput <- matInput[-which(nonFuctionalSeqs),]
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163 # germlines <- germlines[-which(nonFuctionalSeqs)]
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164 # germlines[1:length(germlines)] <- 1:length(germlines)
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165 # groups <- groups[-which(nonFuctionalSeqs)]
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166 # }
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167 #
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168 # if(class(matInput)=="character"){
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169 # write.table("All unproductive seqs",file=paste(outputPath,outputID,".txt",sep=""),quote=F,sep="\t",row.names=F,col.names=T)
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170 # q()
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171 # }
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172 #
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173 # if(nrow(matInput)<10 | is.null(nrow(matInput))){
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174 # write.table(paste(nrow(matInput), "seqs only",sep=""),file=paste(outputPath,outputID,".txt",sep=""),quote=F,sep="\t",row.names=F,col.names=T)
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175 # q()
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176 # }
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177
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178 # replace leading & trailing "-" with "N:
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179 matInput <- t(apply(matInput,1,replaceLeadingTrailingDashes,readEnd))
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180
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181 # Trim (nucleotide) input sequences to the last codon
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182 #matInput[,1] <- apply(matrix(matInput[,1]),1,trimToLastCodon)
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183
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184 # # Check for Indels
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185 # if(fixIndels){
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186 # delPos <- fixDeletions(matInput)
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187 # insPos <- fixInsertions(matInput)
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188 # }else{
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189 # # Check for indels
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190 # indelPos <- checkForInDels(matInput)
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191 # indelPos <- apply(cbind(indelPos[[1]],indelPos[[2]]),1,function(x){(x[1]==T & x[2]==T)})
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192 # }
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193
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194 # If indels are present, remove mutations in the seqeunce & throw warning at end
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195 #matInput[indelPos,] <- apply(matrix(matInput[indelPos,],nrow=sum(indelPos),ncol=2),1,function(x){x[1]=x[2]; return(x) })
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196
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197 colnames(matInput)=c("Input","Germline")
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198
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199 # If seqeunces are clonal, create effective sequence for each clone & modify germline/group definitions
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200 germlinesOriginal = NULL
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201 if(clonal){
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202 germlinesOriginal <- germlines
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203 collapseCloneResults <- tapply(1:nrow(matInput),germlines,function(i){
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204 collapseClone(matInput[i,1],matInput[i[1],2],readEnd,nonTerminalOnly=(clonal-1))
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205 })
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206 matInput = t(sapply(collapseCloneResults,function(x){return(x[[1]])}))
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207 names_groups = tapply(groups,germlines,function(x){names(x[1])})
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208 groups = tapply(groups,germlines,function(x){array(x[1],dimnames=names(x[1]))})
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209 names(groups) = names_groups
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210
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211 names_germlines = tapply(germlines,germlines,function(x){names(x[1])})
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212 germlines = tapply( germlines,germlines,function(x){array(x[1],dimnames=names(x[1]))} )
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213 names(germlines) = names_germlines
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214 matInputErrors = sapply(collapseCloneResults,function(x){return(x[[2]])})
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215 }
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216
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217
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218 # Selection Analysis
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219
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220
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221 # if (length(germlines)>sequenceLimit) {
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222 # # Code to parallelize processing goes here
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223 # stop( paste("Error: Cannot process more than ", Upper_limit," sequences",sep="") )
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224 # }
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225
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226 # if (length(germlines)<sequenceLimit) {}
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227
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228 # Compute expected mutation frequencies
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229 matExpected <- getExpectedIndividual(matInput)
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230
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231 # Count observed number of mutations in the different regions
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232 mutations <- lapply( 1:nrow(matInput), function(i){
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233 #cat(i,"\n")
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234 seqI = s2c(matInput[i,1])
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235 seqG = s2c(matInput[i,2])
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236 matIGL = matrix(c(seqI,seqG),ncol=length(seqI),nrow=2,byrow=T)
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237 retVal <- NA
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238 tryCatch(
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239 retVal <- analyzeMutations2NucUri(matIGL)
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240 , error = function(ex){
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241 retVal <- NA
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242 }
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243 )
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244
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245
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246 return( retVal )
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247 })
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248
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249 matObserved <- t(sapply( mutations, processNucMutations2 ))
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250 numberOfSeqsWithMutations <- numberOfSeqsWithMutations(matObserved, testID)
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251
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252 #if(sum(numberOfSeqsWithMutations)==0){
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253 # write.table("No mutated sequences",file=paste(outputPath,outputID,".txt",sep=""),quote=F,sep="\t",row.names=F,col.names=T)
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254 # q()
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255 #}
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256
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257 matMutationInfo <- cbind(matObserved,matExpected)
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258 rm(matObserved,matExpected)
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259
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260
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261 #Bayesian PDFs
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262 bayes_pdf = computeBayesianScore(matMutationInfo, test=testName, max_sigma=20,length_sigma=4001)
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263 bayesPDF_cdr = bayes_pdf[[1]]
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264 bayesPDF_fwr = bayes_pdf[[2]]
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265 rm(bayes_pdf)
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266
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267 bayesPDF_germlines_cdr = tapply(bayesPDF_cdr,germlines,function(x) groupPosteriors(x,length_sigma=4001))
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268 bayesPDF_germlines_fwr = tapply(bayesPDF_fwr,germlines,function(x) groupPosteriors(x,length_sigma=4001))
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269
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270 bayesPDF_groups_cdr = tapply(bayesPDF_cdr,groups,function(x) groupPosteriors(x,length_sigma=4001))
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271 bayesPDF_groups_fwr = tapply(bayesPDF_fwr,groups,function(x) groupPosteriors(x,length_sigma=4001))
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272
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273 if(lenGroups>1){
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274 groups <- c(groups,lenGroups+1)
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275 names(groups)[length(groups)] = "All sequences combined"
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276 bayesPDF_groups_cdr[[lenGroups+1]] = groupPosteriors(bayesPDF_groups_cdr,length_sigma=4001)
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277 bayesPDF_groups_fwr[[lenGroups+1]] = groupPosteriors(bayesPDF_groups_fwr,length_sigma=4001)
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278 }
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279
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280 #Bayesian Outputs
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281 bayes_cdr = t(sapply(bayesPDF_cdr,calcBayesOutputInfo))
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282 bayes_fwr = t(sapply(bayesPDF_fwr,calcBayesOutputInfo))
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283 bayes_germlines_cdr = t(sapply(bayesPDF_germlines_cdr,calcBayesOutputInfo))
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284 bayes_germlines_fwr = t(sapply(bayesPDF_germlines_fwr,calcBayesOutputInfo))
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285 bayes_groups_cdr = t(sapply(bayesPDF_groups_cdr,calcBayesOutputInfo))
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286 bayes_groups_fwr = t(sapply(bayesPDF_groups_fwr,calcBayesOutputInfo))
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287
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288 #P-values
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289 simgaP_cdr = sapply(bayesPDF_cdr,computeSigmaP)
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290 simgaP_fwr = sapply(bayesPDF_fwr,computeSigmaP)
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291
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292 simgaP_germlines_cdr = sapply(bayesPDF_germlines_cdr,computeSigmaP)
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293 simgaP_germlines_fwr = sapply(bayesPDF_germlines_fwr,computeSigmaP)
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294
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295 simgaP_groups_cdr = sapply(bayesPDF_groups_cdr,computeSigmaP)
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296 simgaP_groups_fwr = sapply(bayesPDF_groups_fwr,computeSigmaP)
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297
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298
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299 #Format output
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300
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301 # Round expected mutation frequencies to 3 decimal places
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302 matMutationInfo[germlinesOriginal[indelPos],] = NA
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303 if(nrow(matMutationInfo)==1){
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304 matMutationInfo[5:8] = round(matMutationInfo[,5:8]/sum(matMutationInfo[,5:8],na.rm=T),3)
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305 }else{
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306 matMutationInfo[,5:8] = t(round(apply(matMutationInfo[,5:8],1,function(x){ return(x/sum(x,na.rm=T)) }),3))
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307 }
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308
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309 listPDFs = list()
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310 nRows = length(unique(groups)) + length(unique(germlines)) + length(groups)
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311
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312 matOutput = matrix(NA,ncol=18,nrow=nRows)
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313 rowNumb = 1
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314 for(G in unique(groups)){
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315 #print(G)
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316 matOutput[rowNumb,c(1,2,11:18)] = c("Group",names(groups)[groups==G][1],bayes_groups_cdr[G,],bayes_groups_fwr[G,],simgaP_groups_cdr[G],simgaP_groups_fwr[G])
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317 listPDFs[[rowNumb]] = list("CDR"=bayesPDF_groups_cdr[[G]],"FWR"=bayesPDF_groups_fwr[[G]])
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318 names(listPDFs)[rowNumb] = names(groups[groups==paste(G)])[1]
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319 #if(names(groups)[which(groups==G)[1]]!="All sequences combined"){
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320 gs = unique(germlines[groups==G])
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321 rowNumb = rowNumb+1
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322 if( !is.na(gs) ){
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323 for( g in gs ){
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324 matOutput[rowNumb,c(1,2,11:18)] = c("Germline",names(germlines)[germlines==g][1],bayes_germlines_cdr[g,],bayes_germlines_fwr[g,],simgaP_germlines_cdr[g],simgaP_germlines_fwr[g])
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325 listPDFs[[rowNumb]] = list("CDR"=bayesPDF_germlines_cdr[[g]],"FWR"=bayesPDF_germlines_fwr[[g]])
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326 names(listPDFs)[rowNumb] = names(germlines[germlines==paste(g)])[1]
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327 rowNumb = rowNumb+1
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328 indexesOfInterest = which(germlines==g)
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329 numbSeqsOfInterest = length(indexesOfInterest)
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330 rowNumb = seq(rowNumb,rowNumb+(numbSeqsOfInterest-1))
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331 matOutput[rowNumb,] = matrix( c( rep("Sequence",numbSeqsOfInterest),
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332 rownames(matInput)[indexesOfInterest],
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333 c(matMutationInfo[indexesOfInterest,1:4]),
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334 c(matMutationInfo[indexesOfInterest,5:8]),
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335 c(bayes_cdr[indexesOfInterest,]),
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336 c(bayes_fwr[indexesOfInterest,]),
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337 c(simgaP_cdr[indexesOfInterest]),
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338 c(simgaP_fwr[indexesOfInterest])
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339 ), ncol=18, nrow=numbSeqsOfInterest,byrow=F)
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340 increment=0
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341 for( ioi in indexesOfInterest){
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342 listPDFs[[min(rowNumb)+increment]] = list("CDR"=bayesPDF_cdr[[ioi]] , "FWR"=bayesPDF_fwr[[ioi]])
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343 names(listPDFs)[min(rowNumb)+increment] = rownames(matInput)[ioi]
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344 increment = increment + 1
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345 }
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346 rowNumb=max(rowNumb)+1
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347
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348 }
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349 }
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350 }
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351 colsToFormat = 11:18
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352 matOutput[,colsToFormat] = formatC( matrix(as.numeric(matOutput[,colsToFormat]), nrow=nrow(matOutput), ncol=length(colsToFormat)) , digits=3)
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353 matOutput[matOutput== " NaN"] = NA
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354
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355
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356
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357 colnames(matOutput) = c("Type", "ID", "Observed_CDR_R", "Observed_CDR_S", "Observed_FWR_R", "Observed_FWR_S",
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358 "Expected_CDR_R", "Expected_CDR_S", "Expected_FWR_R", "Expected_FWR_S",
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359 paste( rep(testName,6), rep(c("Sigma","CIlower","CIupper"),2),rep(c("CDR","FWR"),each=3), sep="_"),
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360 paste( rep(testName,2), rep("P",2),c("CDR","FWR"), sep="_")
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361 )
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362 fileName = paste(outputPath,outputID,".txt",sep="")
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363 write.table(matOutput,file=fileName,quote=F,sep="\t",row.names=T,col.names=NA)
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364 fileName = paste(outputPath,outputID,".RData",sep="")
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365 save(listPDFs,file=fileName)
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366
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367 indelWarning = FALSE
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368 if(sum(indelPos)>0){
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369 indelWarning = "<P>Warning: The following sequences have either gaps and/or deletions, and have been ommited from the analysis.";
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370 indelWarning = paste( indelWarning , "<UL>", sep="" )
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371 for(indels in names(indelPos)[indelPos]){
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372 indelWarning = paste( indelWarning , "<LI>", indels, "</LI>", sep="" )
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373 }
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374 indelWarning = paste( indelWarning , "</UL></P>", sep="" )
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375 }
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376
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377 cloneWarning = FALSE
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378 if(clonal==1){
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379 if(sum(matInputErrors)>0){
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380 cloneWarning = "<P>Warning: The following clones have sequences of unequal length.";
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381 cloneWarning = paste( cloneWarning , "<UL>", sep="" )
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382 for(clone in names(matInputErrors)[matInputErrors]){
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383 cloneWarning = paste( cloneWarning , "<LI>", names(germlines)[as.numeric(clone)], "</LI>", sep="" )
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384 }
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385 cloneWarning = paste( cloneWarning , "</UL></P>", sep="" )
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386 }
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387 }
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388 cat(paste("Success",outputID,indelWarning,cloneWarning,sep="|"))
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