changeset 18:15cb5a49cdbc

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergeXenaMutation.py	Fri Mar 20 18:08:54 2015 -0400
@@ -0,0 +1,212 @@
+#!/usr/bin/env python
+
+import argparse
+import string, os, sys
+
+requiredCOLs = ["chr", "start","end","reference","alt","gene","effect"]
+
+def headerError(filename, column, ferror):
+  ferror.write(filename +" does not have column " + column+"\n")
+  ferror.close()
+  sys.exit(1)
+
+def findAnyValueInList (values, dataList):
+  for value in values:
+    for i in range(0,len(dataList)):
+      if value == dataList[i]:
+        return i
+  return -1
+
+def header (infile, ferror):
+  fin= open(infile,'U')
+
+  columnDic ={}
+  #header
+  line = fin.readline()
+  fin.close()
+  if line [0]=="#":
+    line = line[1:-1]
+  data = string.split(line,"\t")
+
+  columnDic["chr"]= findAnyValueInList (["chr","chrom"], data)
+  if columnDic["chr"] ==-1:
+    headerError(infile, "chr", ferror)
+
+  columnDic["start"]= findAnyValueInList (["start","chrStart"], data)
+  if columnDic["start"] == -1:
+    headerError(infile, "start", ferror)
+
+  columnDic["end"]= findAnyValueInList (["end","chrEnd"], data)
+  if columnDic["end"] == -1:
+    headerError(infile, "end", ferror)
+
+  columnDic["alt"]= findAnyValueInList (["alt"], data)
+  if columnDic["alt"] == -1:
+    headerError(infile, "alt", ferror)
+
+  columnDic["reference"]= findAnyValueInList (["reference","ref"], data)
+  if columnDic["reference"] == -1:
+    headerError(infile, "reference", ferror)
+
+  columnDic["gene"]= findAnyValueInList (["gene"], data)
+  if columnDic["gene"] == -1:
+    headerError(infile, "gene", ferror)
+
+  columnDic["effect"]= findAnyValueInList (["effect"], data)
+  if columnDic["effect"] == -1:
+    headerError(infile, "effect", ferror)
+
+  requiredCols = columnDic.keys()
+  requiredColsPos = columnDic.values()
+  for i in range(1,len(data)):
+    if i not in requiredColsPos:
+      columnDic [data[i]]=i
+
+  return columnDic
+
+def summarizeColumns(infiles, fileColumn, allCols, ferror):
+  for infile in inFiles:
+    columnDic = header (infile, ferror)
+    fileColumn [infile] = columnDic
+    for col in columnDic:
+      if col not in allCols:
+        allCols.append(col)
+  return
+
+def outputHeader (requiredCOLs,allCols,fout):
+  fout.write("#sample")
+  for col in requiredCOLs:
+    fout.write("\t"+col)
+  for col in allCols:
+    if col not in requiredCOLs:
+      fout.write("\t"+col)
+  fout.write("\n")
+  fout.close()
+  return
+
+def processAndOutput(infile,requiredCOLs,allCols,columnDic,fout):
+  fin = open(infile,'U')
+  fin.readline()
+  while 1:
+    line = fin.readline()[:-1]
+    if line =="":
+      break
+    data = string.split(line,'\t')
+    fout.write(data[0])
+    for col in requiredCOLs:
+      pos = columnDic[col]
+      fout.write("\t"+ data[pos])
+    for col in allCols:
+      if col not in requiredCOLs:
+        if col in columnDic:
+          pos = columnDic[col]
+          fout.write("\t"+ data[pos])
+        else:
+          fout.write("\t")
+    fout.write("\n")
+  fin.close()
+  return
+
+def collectSource(inFile, label, sampleDic):
+  fin = open(inFile,'U')
+  fin.readline()
+  while 1:
+    line = fin.readline()[:-1]
+    if line =="":
+      break
+    sample = string.split(line,'\t')[0]
+    if sample not in sampleDic:
+      sampleDic[sample]=[]
+    if inFile not in sampleDic[sample]:
+      sampleDic[sample].append(label)
+  fin.close()
+  return
+
+def outputSampleDic (sampleDic, outPhenotypeFile):
+  fout = open(outPhenotypeFile,'w')
+  fout.write("sample\tsource\n")
+  for sample in sampleDic:
+    source = sampleDic[sample]
+    source.sort()
+    fout.write(sample+"\t"+string.join(source,", ")+"\n")
+  fout.close()
+  return
+
+if __name__ == '__main__' :
+  if len(sys.argv[:]) <6:
+    print "python mergeMultipleXenaMutation.py outputXenaMutation outputPhenotypeMatrix errorLog inputfile(s)"
+    print "this is merging data A+B=C for mutation by position type of data\n"
+    sys.exit(1)
+
+    #
+    # The input files to this script are two or more matrices, in which
+    # columns represent samples and rows represent genes or measurements.
+    # There are two output files: outMergedData contains the input data merged
+    # into a single matrix, and outSourceMatrix is a two-column matrix
+    # indicating which file each sample (or column label) came from.  This
+    # assumes that each sample came from at most one file.
+    #
+    parser = argparse.ArgumentParser()
+    parser.add_argument("inFileA", type=str, help="First input file")
+    parser.add_argument("inFileB", type=str, help="Second input file")
+    parser.add_argument("outMergedData", type=str,
+                        help="Filename for the merged dataset")
+    parser.add_argument("outSourceMatrix", type=str,
+                        help="""Filename for a Nx2 matrix that indicates
+                                the source file of each column""")
+    parser.add_argument("errorLog", type=str,
+                        help="""Error log""")
+    parser.add_argument("--aLabel", type=str, default=None,
+                        help="User-friendly label for the first input file")
+    parser.add_argument("--bLabel", type=str, default=None,
+                        help="User-friendly label for the second input file")
+    args = parser.parse_args()
+
+                                    
+    #inFiles = sys.argv[4:]
+    print inFiles
+    errofile = args.errorLog
+    outfile = args.outMergedData
+    print outfile
+    outPhenotypeFile = args.outSourceMatrix
+    print outPhenotypeFile
+    
+    ferror = open(errofile,'w')
+    
+    #get all the columns, build fileColumn dictionary
+    fileColumn={}
+    allCols =[]
+    summarizeColumns(inFiles, fileColumn, allCols, ferror)
+    ferror.close()
+
+    #output header line
+    fout = open(outfile,'w')
+    outputHeader (requiredCOLs,allCols,fout)
+
+    #process and output combined mutationXena file
+    fout = open(outfile,'a')
+
+    columnDic = fileColumn[args.inFileA]
+    processAndOutput(args.inFileA,requiredCOLs,allCols,columnDic,fout)
+    columnDic = fileColumn[args.inFileB]
+    processAndOutput(args.inFileB,requiredCOLs,allCols,columnDic,fout)
+    fout.close()
+
+    #collect sample from source information
+    sampleDic ={}
+    if args.aLabel is None:
+      collectSource(args.inFileA, args.inFileA, sampleDic)
+    else:
+      collectSource(args.inFileA, args.aLabel, sampleDic
+    if args.bLabel is None:
+      collectSource(args.inFileB, args.inFileB, sampleDic)
+    else:
+      collectSource(args.inFileB, args.bLabel, sampleDic
+
+
+    #output sample source information as phenotype matrix
+    outputSampleDic (sampleDic, outPhenotypeFile)
+
+
+
+