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18
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import string, os, sys
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5
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6 requiredCOLs = ["chr", "start","end","reference","alt","gene","effect"]
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7
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8 def headerError(filename, column, ferror):
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9 ferror.write(filename +" does not have column " + column+"\n")
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10 ferror.close()
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11 sys.exit(1)
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12
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13 def findAnyValueInList (values, dataList):
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14 for value in values:
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15 for i in range(0,len(dataList)):
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16 if value == dataList[i]:
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17 return i
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18 return -1
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19
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20 def header (infile, ferror):
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21 fin= open(infile,'U')
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22
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23 columnDic ={}
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24 #header
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25 line = fin.readline()
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26 fin.close()
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27 if line [0]=="#":
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28 line = line[1:-1]
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29 data = string.split(line,"\t")
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30
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31 columnDic["chr"]= findAnyValueInList (["chr","chrom"], data)
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32 if columnDic["chr"] ==-1:
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33 headerError(infile, "chr", ferror)
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34
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35 columnDic["start"]= findAnyValueInList (["start","chrStart"], data)
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36 if columnDic["start"] == -1:
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37 headerError(infile, "start", ferror)
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38
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39 columnDic["end"]= findAnyValueInList (["end","chrEnd"], data)
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40 if columnDic["end"] == -1:
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41 headerError(infile, "end", ferror)
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42
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43 columnDic["alt"]= findAnyValueInList (["alt"], data)
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44 if columnDic["alt"] == -1:
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45 headerError(infile, "alt", ferror)
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46
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47 columnDic["reference"]= findAnyValueInList (["reference","ref"], data)
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48 if columnDic["reference"] == -1:
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49 headerError(infile, "reference", ferror)
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50
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51 columnDic["gene"]= findAnyValueInList (["gene"], data)
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52 if columnDic["gene"] == -1:
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53 headerError(infile, "gene", ferror)
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54
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55 columnDic["effect"]= findAnyValueInList (["effect"], data)
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56 if columnDic["effect"] == -1:
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57 headerError(infile, "effect", ferror)
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58
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59 requiredCols = columnDic.keys()
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60 requiredColsPos = columnDic.values()
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61 for i in range(1,len(data)):
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62 if i not in requiredColsPos:
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63 columnDic [data[i]]=i
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64
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65 return columnDic
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66
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20
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67 def summarizeColumns(inFiles, fileColumn, allCols, ferror):
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18
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68 for infile in inFiles:
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69 columnDic = header (infile, ferror)
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70 fileColumn [infile] = columnDic
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71 for col in columnDic:
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72 if col not in allCols:
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73 allCols.append(col)
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74 return
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75
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76 def outputHeader (requiredCOLs,allCols,fout):
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77 fout.write("#sample")
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78 for col in requiredCOLs:
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79 fout.write("\t"+col)
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80 for col in allCols:
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81 if col not in requiredCOLs:
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82 fout.write("\t"+col)
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83 fout.write("\n")
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84 fout.close()
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85 return
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86
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87 def processAndOutput(infile,requiredCOLs,allCols,columnDic,fout):
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88 fin = open(infile,'U')
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89 fin.readline()
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90 while 1:
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91 line = fin.readline()[:-1]
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92 if line =="":
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93 break
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94 data = string.split(line,'\t')
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95 fout.write(data[0])
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96 for col in requiredCOLs:
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97 pos = columnDic[col]
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98 fout.write("\t"+ data[pos])
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99 for col in allCols:
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100 if col not in requiredCOLs:
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101 if col in columnDic:
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102 pos = columnDic[col]
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103 fout.write("\t"+ data[pos])
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104 else:
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105 fout.write("\t")
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106 fout.write("\n")
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107 fin.close()
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108 return
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109
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110 def collectSource(inFile, label, sampleDic):
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111 fin = open(inFile,'U')
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112 fin.readline()
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113 while 1:
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114 line = fin.readline()[:-1]
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115 if line =="":
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116 break
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117 sample = string.split(line,'\t')[0]
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118 if sample not in sampleDic:
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119 sampleDic[sample]=[]
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120 if inFile not in sampleDic[sample]:
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121 sampleDic[sample].append(label)
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122 fin.close()
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123 return
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124
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125 def outputSampleDic (sampleDic, outPhenotypeFile):
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126 fout = open(outPhenotypeFile,'w')
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127 fout.write("sample\tsource\n")
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128 for sample in sampleDic:
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129 source = sampleDic[sample]
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130 source.sort()
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131 fout.write(sample+"\t"+string.join(source,", ")+"\n")
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132 fout.close()
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133 return
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134
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135 if __name__ == '__main__' :
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136 if len(sys.argv[:]) <6:
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137 print "python mergeMultipleXenaMutation.py outputXenaMutation outputPhenotypeMatrix errorLog inputfile(s)"
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138 print "this is merging data A+B=C for mutation by position type of data\n"
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139 sys.exit(1)
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140
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20
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141 #
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142 # The input files to this script are two or more matrices, in which
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143 # columns represent samples and rows represent genes or measurements.
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144 # There are two output files: outMergedData contains the input data merged
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145 # into a single matrix, and outSourceMatrix is a two-column matrix
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146 # indicating which file each sample (or column label) came from. This
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147 # assumes that each sample came from at most one file.
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148 #
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149 parser = argparse.ArgumentParser()
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150 parser.add_argument("outMergedData", type=str,
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151 help="Filename for the merged dataset")
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152 parser.add_argument("outSourceMatrix", type=str,
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153 help="""Filename for a Nx2 matrix that indicates
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154 the source file of each column""")
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155 parser.add_argument("errorLog", type=str,
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156 help="""Error log""")
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157 parser.add_argument("inFileA", type=str, help="First input file")
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158 parser.add_argument("inFileB", type=str, help="Second input file")
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159 parser.add_argument("--aLabel", type=str, default=None,
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160 help="User-friendly label for the first input file")
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161 parser.add_argument("--bLabel", type=str, default=None,
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162 help="User-friendly label for the second input file")
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163 args = parser.parse_args()
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164
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165
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166 #inFiles = sys.argv[4:]
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167 inFiles = list()
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168 inFiles.append(args.inFileA)
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169 inFiles.append(args.inFileB)
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170 errofile = args.errorLog
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171 outfile = args.outMergedData
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172 #print outfile
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173 outPhenotypeFile = args.outSourceMatrix
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174 #print outPhenotypeFile
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175
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176 ferror = open(errofile,'w')
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177
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178 #get all the columns, build fileColumn dictionary
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179 fileColumn={}
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180 allCols =[]
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181 summarizeColumns(inFiles, fileColumn, allCols, ferror)
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182 ferror.close()
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183
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184 #output header line
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185 fout = open(outfile,'w')
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186 outputHeader (requiredCOLs,allCols,fout)
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187
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188 #process and output combined mutationXena file
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189 fout = open(outfile,'a')
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190
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191 columnDic = fileColumn[args.inFileA]
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192 processAndOutput(args.inFileA,requiredCOLs,allCols,columnDic,fout)
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193 columnDic = fileColumn[args.inFileB]
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194 processAndOutput(args.inFileB,requiredCOLs,allCols,columnDic,fout)
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195 fout.close()
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196
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197 #collect sample from source information
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198 sampleDic ={}
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199 if args.aLabel is None:
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200 collectSource(args.inFileA, args.inFileA, sampleDic)
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201 else:
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202 collectSource(args.inFileA, args.aLabel, sampleDic)
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203 if args.bLabel is None:
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204 collectSource(args.inFileB, args.inFileB, sampleDic)
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205 else:
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206 collectSource(args.inFileB, args.bLabel, sampleDic)
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207
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208
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209 #output sample source information as phenotype matrix
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210 outputSampleDic (sampleDic, outPhenotypeFile)
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211
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212
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213
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214
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