Mercurial > repos > guerler > dbkit
diff dbkit_extract.py @ 2:81c7d4668a7e draft
"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author | guerler |
---|---|
date | Wed, 16 Dec 2020 12:02:48 +0000 |
parents | |
children | 03e124ff7e26 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbkit_extract.py Wed Dec 16 12:02:48 2020 +0000 @@ -0,0 +1,45 @@ +#! /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 + entries = list() + with open(args.list, "r") as f: + for line in f: + name = line.split()[0] + entries.append(name) + logFile.write("Detected %s entries.\n" % len(entries)) + tempFile = "temp.dat" + count = 0 + dbkit = DBKit(args.index, args.database) + for entry in sorted(entries): + success = dbkit.createFile(entry, tempFile) + if success: + currentSize = getsize(outData) + entrySize = getsize(tempFile) + system("cat %s >> %s" % (tempFile, outData)) + system("echo '%s\t%s\t%s' >> %s" % (entry, currentSize, entrySize, outIndex)) + count = count + 1 + else: + logFile.write("Entry %s not found.\n" % entry) + logFile.write("Extracted %s entries.\n" % count) + logFile.close() + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='DBKit - Merge database pair.') + parser.add_argument('-l', '--list', help='List of entries to be extracted', required=True) + parser.add_argument('-i', '--index', help='Database Index file (ffindex)', required=True) + parser.add_argument('-d', '--database', help='Database Data file (ffdata)', 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('-g', '--log', help='Log file', required=True) + args = parser.parse_args() + main(args)