Mercurial > repos > guerler > dbkit
view dbkit_merge.py @ 2:81c7d4668a7e draft
"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author | guerler |
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date | Wed, 16 Dec 2020 12:02:48 +0000 |
parents | |
children | 03e124ff7e26 |
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#! /usr/bin/env python3 import argparse from os import system from os.path import getsize from dbkit_package.DBKit import DBKit def main(args): logFile = open(args.log, "w") outIndex = args.outindex outData = args.outdata if getsize(args.firstindex) > getsize(args.secondindex): firstIndex = args.firstindex firstData = args.firstdata secondIndex = args.secondindex secondData = args.seconddata else: firstIndex = args.secondindex firstData = args.seconddata secondIndex = args.firstindex secondData = args.firstdata system("cp %s %s" % (firstIndex, outIndex)) system("cp %s %s" % (firstData, outData)) firstEntries = set() with open(firstIndex, "r") as f: for line in f: name = line.split()[0] firstEntries.add(name) logFile.write("Detected %s entries.\n" % len(firstEntries)) secondEntries = list() with open(secondIndex, "r") as f: for line in f: name = line.split()[0] secondEntries.append(name) tempFile = "temp.dat" count = 0 dbkit = DBKit(secondIndex, secondData) for secondKey in secondEntries: if secondKey not in firstEntries: dbkit.createFile(secondKey, tempFile) entrySize = getsize(tempFile) currentSize = getsize(outData) system("cat %s >> %s" % (tempFile, outData)) system("echo '%s\t%s\t%s' >> %s" % (secondKey, currentSize, entrySize, outIndex)) count = count + 1 else: logFile.write("Skipping existing entry %s.\n" % secondKey) logFile.write("Added %s entries.\n" % count) logFile.close() if __name__ == "__main__": parser = argparse.ArgumentParser(description='DBKit - Merge database pair.') parser.add_argument('-fi', '--firstindex', help='First Index file', required=True) parser.add_argument('-fd', '--firstdata', help='First Data file', required=True) parser.add_argument('-si', '--secondindex', help='Second Index file', required=True) parser.add_argument('-sd', '--seconddata', help='Second Data file', required=True) parser.add_argument('-oi', '--outindex', help='Output Index file', required=True) parser.add_argument('-od', '--outdata', help='Output Data file', required=True) parser.add_argument('-log', '--log', help='Log file', required=True) args = parser.parse_args() main(args)