import sys

def main(argv=None):
    if not argv:
        argv = sys.argv

    linkerfile = argv[1]
    infile = argv[2]
    outfile = argv[3]

    markLinkers(linkerfile, infile, outfile)


def markLinkers(linkerFileName, inFileName, outFileName):
    infile = open(inFileName)
    outfile = open(outFileName, "w")
    linkerDict, linkerList = getLinkerInformationFromFile(linkerFileName)

    for line in infile:
        if len(line) < 2:
            continue

        if "@" in line:
            readID = line.strip()
            readID = readID.replace("@", "")
        else:
            found = False
            for linkerID in linkerList:
                position = line.find(linkerDict[linkerID])
                if position >= 19:
                    found = True
                    outfile.write(">L%s_%s\n" % (linkerID[-1:], readID))
                    outfile.write("%s\n" % line[:20])

                if not found:
                    outfile.write(">NA_%s\n" % readID)
                    outfile.write("%s\n" % line[:20])


def getLinkerInformationFromFile(linkerFileName):
    linkerDict = {}
    linkerList = []
    try:
        linkerfile = open(linkerFileName)
        return getLinkerInformation(linkerfile)
    except IOError:
        return linkerDict, linkerList


def getLinkerInformation(linkerInformationList):
    linkerDict = {}
    linkerList = []

    for entry in linkerInformationList:
        if ">" in entry:
            linkerID = entry.strip()
            linkerID = linkerID[1:]
            linkerList.append(linkerID)
        else:
            sequence = entry.strip()
            linkerDict[linkerID] = sequence[:10]

    return linkerDict, linkerList



if __name__ == "__main__":
    main(sys.argv)