Mercurial > repos > melissacline > ucsc_cancer_utilities
annotate mergeXenaMutation.py @ 57:eef100efcc4c
fix
| author | jingchunzhu |
|---|---|
| date | Fri, 18 Sep 2015 11:11:15 -0700 |
| parents | 1093078e7976 |
| children |
| rev | line source |
|---|---|
| 18 | 1 #!/usr/bin/env python |
| 2 | |
| 3 import argparse | |
| 4 import string, os, sys | |
| 5 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
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6 requiredCOLs = ["chr", "start","end","reference","alt"] |
| 18 | 7 |
| 8 def headerError(filename, column, ferror): | |
| 9 ferror.write(filename +" does not have column " + column+"\n") | |
| 10 ferror.close() | |
| 11 sys.exit(1) | |
| 12 | |
| 13 def findAnyValueInList (values, dataList): | |
| 14 for value in values: | |
| 15 for i in range(0,len(dataList)): | |
| 16 if value == dataList[i]: | |
| 17 return i | |
| 18 return -1 | |
| 19 | |
| 20 def header (infile, ferror): | |
| 21 fin= open(infile,'U') | |
| 22 | |
| 23 columnDic ={} | |
| 24 #header | |
| 25 line = fin.readline() | |
| 26 fin.close() | |
| 27 if line [0]=="#": | |
| 28 line = line[1:-1] | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
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changeset
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29 data = string.split(string.strip(line),"\t") |
| 18 | 30 |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
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diff
changeset
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31 columnDic["chr"]= findAnyValueInList (["chr","chrom", "Chr"], data) |
| 18 | 32 if columnDic["chr"] ==-1: |
| 33 headerError(infile, "chr", ferror) | |
| 34 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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35 columnDic["start"]= findAnyValueInList (["start","chrStart","Start"], data) |
| 18 | 36 if columnDic["start"] == -1: |
| 37 headerError(infile, "start", ferror) | |
| 38 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
|
39 columnDic["end"]= findAnyValueInList (["end","chrEnd", "End"], data) |
| 18 | 40 if columnDic["end"] == -1: |
| 41 headerError(infile, "end", ferror) | |
| 42 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
|
43 columnDic["alt"]= findAnyValueInList (["alt","Alt"], data) |
| 18 | 44 if columnDic["alt"] == -1: |
| 45 headerError(infile, "alt", ferror) | |
| 46 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
|
47 columnDic["reference"]= findAnyValueInList (["reference","ref","Reference","Ref"], data) |
| 18 | 48 if columnDic["reference"] == -1: |
| 49 headerError(infile, "reference", ferror) | |
| 50 | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
|
51 #columnDic["gene"]= findAnyValueInList (["gene","Gene"], data) |
|
1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
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diff
changeset
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52 #if columnDic["gene"] == -1: |
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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53 # headerError(infile, "gene", ferror) |
| 18 | 54 |
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55
1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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55 #columnDic["effect"]= findAnyValueInList (["effect"], data) |
|
1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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56 #if columnDic["effect"] == -1: |
|
1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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57 # headerError(infile, "effect", ferror) |
| 18 | 58 |
| 59 requiredCols = columnDic.keys() | |
| 60 requiredColsPos = columnDic.values() | |
| 61 for i in range(1,len(data)): | |
| 62 if i not in requiredColsPos: | |
| 63 columnDic [data[i]]=i | |
| 64 | |
| 65 return columnDic | |
| 66 | |
| 20 | 67 def summarizeColumns(inFiles, fileColumn, allCols, ferror): |
| 18 | 68 for infile in inFiles: |
| 69 columnDic = header (infile, ferror) | |
| 70 fileColumn [infile] = columnDic | |
| 71 for col in columnDic: | |
| 72 if col not in allCols: | |
| 73 allCols.append(col) | |
| 74 return | |
| 75 | |
| 76 def outputHeader (requiredCOLs,allCols,fout): | |
|
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1093078e7976
merge mutation data conform to new mutationVector data standard
jingchunzhu
parents:
41
diff
changeset
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77 fout.write("sample") |
| 18 | 78 for col in requiredCOLs: |
| 79 fout.write("\t"+col) | |
| 80 for col in allCols: | |
| 81 if col not in requiredCOLs: | |
| 82 fout.write("\t"+col) | |
| 83 fout.write("\n") | |
| 84 fout.close() | |
| 85 return | |
| 86 | |
| 87 def processAndOutput(infile,requiredCOLs,allCols,columnDic,fout): | |
| 88 fin = open(infile,'U') | |
| 89 fin.readline() | |
| 90 while 1: | |
| 91 line = fin.readline()[:-1] | |
| 92 if line =="": | |
| 93 break | |
| 94 data = string.split(line,'\t') | |
| 95 fout.write(data[0]) | |
| 96 for col in requiredCOLs: | |
| 97 pos = columnDic[col] | |
| 98 fout.write("\t"+ data[pos]) | |
| 99 for col in allCols: | |
| 100 if col not in requiredCOLs: | |
| 101 if col in columnDic: | |
| 102 pos = columnDic[col] | |
| 103 fout.write("\t"+ data[pos]) | |
| 104 else: | |
| 105 fout.write("\t") | |
| 106 fout.write("\n") | |
| 107 fin.close() | |
| 108 return | |
| 109 | |
| 110 def collectSource(inFile, label, sampleDic): | |
| 111 fin = open(inFile,'U') | |
| 112 fin.readline() | |
| 113 while 1: | |
| 114 line = fin.readline()[:-1] | |
| 115 if line =="": | |
| 116 break | |
| 117 sample = string.split(line,'\t')[0] | |
| 118 if sample not in sampleDic: | |
| 119 sampleDic[sample]=[] | |
| 41 | 120 if label not in sampleDic[sample]: |
| 18 | 121 sampleDic[sample].append(label) |
| 122 fin.close() | |
| 123 return | |
| 124 | |
| 125 def outputSampleDic (sampleDic, outPhenotypeFile): | |
| 126 fout = open(outPhenotypeFile,'w') | |
| 127 fout.write("sample\tsource\n") | |
| 128 for sample in sampleDic: | |
| 129 source = sampleDic[sample] | |
| 130 source.sort() | |
| 131 fout.write(sample+"\t"+string.join(source,", ")+"\n") | |
| 132 fout.close() | |
| 133 return | |
| 134 | |
| 135 if __name__ == '__main__' : | |
| 136 if len(sys.argv[:]) <6: | |
| 137 print "python mergeMultipleXenaMutation.py outputXenaMutation outputPhenotypeMatrix errorLog inputfile(s)" | |
| 138 print "this is merging data A+B=C for mutation by position type of data\n" | |
| 139 sys.exit(1) | |
| 140 | |
| 20 | 141 # |
| 142 # The input files to this script are two or more matrices, in which | |
| 143 # columns represent samples and rows represent genes or measurements. | |
| 144 # There are two output files: outMergedData contains the input data merged | |
| 145 # into a single matrix, and outSourceMatrix is a two-column matrix | |
| 146 # indicating which file each sample (or column label) came from. This | |
| 147 # assumes that each sample came from at most one file. | |
| 148 # | |
| 149 parser = argparse.ArgumentParser() | |
| 150 parser.add_argument("outMergedData", type=str, | |
| 151 help="Filename for the merged dataset") | |
| 152 parser.add_argument("outSourceMatrix", type=str, | |
| 153 help="""Filename for a Nx2 matrix that indicates | |
| 18 | 154 the source file of each column""") |
| 20 | 155 parser.add_argument("errorLog", type=str, |
| 156 help="""Error log""") | |
| 157 parser.add_argument("inFileA", type=str, help="First input file") | |
| 158 parser.add_argument("inFileB", type=str, help="Second input file") | |
| 159 parser.add_argument("--aLabel", type=str, default=None, | |
| 160 help="User-friendly label for the first input file") | |
| 161 parser.add_argument("--bLabel", type=str, default=None, | |
| 162 help="User-friendly label for the second input file") | |
| 163 args = parser.parse_args() | |
| 18 | 164 |
| 165 | |
| 20 | 166 #inFiles = sys.argv[4:] |
| 167 inFiles = list() | |
| 168 inFiles.append(args.inFileA) | |
| 169 inFiles.append(args.inFileB) | |
| 170 errofile = args.errorLog | |
| 171 outfile = args.outMergedData | |
| 172 #print outfile | |
| 173 outPhenotypeFile = args.outSourceMatrix | |
| 174 #print outPhenotypeFile | |
| 18 | 175 |
| 20 | 176 ferror = open(errofile,'w') |
| 177 | |
| 178 #get all the columns, build fileColumn dictionary | |
| 179 fileColumn={} | |
| 180 allCols =[] | |
| 181 summarizeColumns(inFiles, fileColumn, allCols, ferror) | |
| 182 ferror.close() | |
| 18 | 183 |
| 20 | 184 #output header line |
| 185 fout = open(outfile,'w') | |
| 186 outputHeader (requiredCOLs,allCols,fout) | |
| 187 | |
| 188 #process and output combined mutationXena file | |
| 189 fout = open(outfile,'a') | |
| 18 | 190 |
| 20 | 191 columnDic = fileColumn[args.inFileA] |
| 192 processAndOutput(args.inFileA,requiredCOLs,allCols,columnDic,fout) | |
| 193 columnDic = fileColumn[args.inFileB] | |
| 194 processAndOutput(args.inFileB,requiredCOLs,allCols,columnDic,fout) | |
| 195 fout.close() | |
| 196 | |
| 197 #collect sample from source information | |
| 198 sampleDic ={} | |
| 199 if args.aLabel is None: | |
| 200 collectSource(args.inFileA, args.inFileA, sampleDic) | |
| 201 else: | |
| 202 collectSource(args.inFileA, args.aLabel, sampleDic) | |
| 203 if args.bLabel is None: | |
| 204 collectSource(args.inFileB, args.inFileB, sampleDic) | |
| 205 else: | |
| 206 collectSource(args.inFileB, args.bLabel, sampleDic) | |
| 18 | 207 |
| 208 | |
| 20 | 209 #output sample source information as phenotype matrix |
| 210 outputSampleDic (sampleDic, outPhenotypeFile) | |
| 18 | 211 |
| 212 | |
| 213 | |
| 214 |