annotate mergeXenaMutation.py @ 37:e81019e3ac99

Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format
author melissacline
date Mon, 27 Jul 2015 16:29:24 -0700
parents 914bc8ee6222
children 9806198df91f
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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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67 def summarizeColumns(inFiles, fileColumn, allCols, ferror):
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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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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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209 #output sample source information as phenotype matrix
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210 outputSampleDic (sampleDic, outPhenotypeFile)
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