diff dbkit_extract.py @ 3:03e124ff7e26 draft

"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author guerler
date Wed, 16 Dec 2020 13:11:35 +0000
parents 81c7d4668a7e
children
line wrap: on
line diff
--- a/dbkit_extract.py	Wed Dec 16 12:02:48 2020 +0000
+++ b/dbkit_extract.py	Wed Dec 16 13:11:35 2020 +0000
@@ -1,31 +1,26 @@
 #! /usr/bin/env python3
 import argparse
-from os import system
-from os.path import getsize
 
-from dbkit_package.DBKit import DBKit
+from dbkit_package.DBKit import DBKit, writeEntry
 
 
 def main(args):
     logFile = open(args.log, "w")
-    outIndex = args.outindex
-    outData = args.outdata
+    outputIndex = args.outputindex
+    outputDatabase = args.outputdatabase
     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"
+    fileName = "temp.dat"
     count = 0
     dbkit = DBKit(args.index, args.database)
     for entry in sorted(entries):
-        success = dbkit.createFile(entry, tempFile)
+        success = dbkit.createFile(entry, fileName)
         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))
+            writeEntry(entry, fileName, outputIndex, outputDatabase)
             count = count + 1
         else:
             logFile.write("Entry %s not found.\n" % entry)
@@ -38,8 +33,8 @@
     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('-oi', '--outputindex', help='Output Index file', required=True)
+    parser.add_argument('-od', '--outputdatabase', help='Output Data file', required=True)
     parser.add_argument('-g', '--log', help='Log file', required=True)
     args = parser.parse_args()
     main(args)