Mercurial > repos > guerler > dbkit

comparison dbkit_merge.py @ 2:81c7d4668a7e draft

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"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author guerler
date Wed, 16 Dec 2020 12:02:48 +0000
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children 03e124ff7e26
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1:987e55ea29b8 2:81c7d4668a7e
1 #! /usr/bin/env python3
2 import argparse
3 from os import system
4 from os.path import getsize
5
6 from dbkit_package.DBKit import DBKit
7
8
9 def main(args):
10 logFile = open(args.log, "w")
11 outIndex = args.outindex
12 outData = args.outdata
13 if getsize(args.firstindex) > getsize(args.secondindex):
14 firstIndex = args.firstindex
15 firstData = args.firstdata
16 secondIndex = args.secondindex
17 secondData = args.seconddata
18 else:
19 firstIndex = args.secondindex
20 firstData = args.seconddata
21 secondIndex = args.firstindex
22 secondData = args.firstdata
23 system("cp %s %s" % (firstIndex, outIndex))
24 system("cp %s %s" % (firstData, outData))
25 firstEntries = set()
26 with open(firstIndex, "r") as f:
27 for line in f:
28 name = line.split()[0]
29 firstEntries.add(name)
30 logFile.write("Detected %s entries.\n" % len(firstEntries))
31 secondEntries = list()
32 with open(secondIndex, "r") as f:
33 for line in f:
34 name = line.split()[0]
35 secondEntries.append(name)
36 tempFile = "temp.dat"
37 count = 0
38 dbkit = DBKit(secondIndex, secondData)
39 for secondKey in secondEntries:
40 if secondKey not in firstEntries:
41 dbkit.createFile(secondKey, tempFile)
42 entrySize = getsize(tempFile)
43 currentSize = getsize(outData)
44 system("cat %s >> %s" % (tempFile, outData))
45 system("echo '%s\t%s\t%s' >> %s" % (secondKey, currentSize, entrySize, outIndex))
46 count = count + 1
47 else:
48 logFile.write("Skipping existing entry %s.\n" % secondKey)
49 logFile.write("Added %s entries.\n" % count)
50 logFile.close()
51
52
53 if __name__ == "__main__":
54 parser = argparse.ArgumentParser(description='DBKit - Merge database pair.')
55 parser.add_argument('-fi', '--firstindex', help='First Index file', required=True)
56 parser.add_argument('-fd', '--firstdata', help='First Data file', required=True)
57 parser.add_argument('-si', '--secondindex', help='Second Index file', required=True)
58 parser.add_argument('-sd', '--seconddata', help='Second Data file', required=True)
59 parser.add_argument('-oi', '--outindex', help='Output Index file', required=True)
60 parser.add_argument('-od', '--outdata', help='Output Data file', required=True)
61 parser.add_argument('-log', '--log', help='Log file', required=True)
62 args = parser.parse_args()
63 main(args)