11 markLinkers(linkerfile, infile, outfile)
14 def markLinkers(linkerFileName, inFileName, outFileName):
15 infile = open(inFileName)
16 outfile = open(outFileName, "w")
17 linkerDict, linkerList = getLinkerInformationFromFile(linkerFileName)
25 readID = readID.replace("@", "")
28 for linkerID in linkerList:
29 position = line.find(linkerDict[linkerID])
32 outfile.write(">L%s_%s\n" % (linkerID[-1:], readID))
33 outfile.write("%s\n" % line[:20])
36 outfile.write(">NA_%s\n" % readID)
37 outfile.write("%s\n" % line[:20])
40 def getLinkerInformationFromFile(linkerFileName):
44 linkerfile = open(linkerFileName)
45 return getLinkerInformation(linkerfile)
47 return linkerDict, linkerList
50 def getLinkerInformation(linkerInformationList):
54 for entry in linkerInformationList:
56 linkerID = entry.strip()
57 linkerID = linkerID[1:]
58 linkerList.append(linkerID)
60 sequence = entry.strip()
61 linkerDict[linkerID] = sequence[:10]
63 return linkerDict, linkerList
66 if __name__ == "__main__":