Mercurial > repos > guerler > dbkit

annotate dbkit_create.py @ 0:1914107cc967 draft

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"planemo upload commit 3632646bec5edbe47e06c894e32bfd215b895555-dirty"
author guerler
date Wed, 25 Nov 2020 17:22:48 +0000
parents
children 987e55ea29b8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1914107cc967 "planemo upload commit 3632646bec5edbe47e06c894e32bfd215b895555-dirty"
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1 #! /usr/bin/env python3
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2 import argparse
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3 from os import system
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4 from os.path import getsize
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5
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6
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7 def getIdentifiers(args):
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8 entries = set()
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9 with open(args.list) as file:
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10 for line in file:
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11 entry = line.split()[0]
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12 idLength = int(args.idlength)
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13 if idLength > 0:
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14 entry = entry[:idLength]
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15 if args.idcase == "lower":
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16 entry = entry.lower()
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17 elif args.idcase == "upper":
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18 entry = entry.upper()
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19 if args.idextension is not None:
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20 entry = "%s.%s" % (entry, args.idextension)
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21 entries.add(entry)
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22 return sorted(entries)
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23
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24
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25 def main(args):
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26 entries = getIdentifiers(args)
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27 logFile = open(args.log, "w")
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28 logFile.write("Found %s entries.\n" % len(entries))
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29 outputIndex = args.index
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30 outputDatabase = args.database
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31 tempPath = args.temp.rstrip("/")
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32 tempFile = "%s/temp.pdb" % tempPath
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33 system("mkdir -p %s" % tempPath)
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34 system("rm -f %s" % outputDatabase)
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35 indexFile = open(outputIndex, 'w')
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36 start = 0
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37 for entryId in entries:
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38 logFile.write("Loading %s.\n" % entryId)
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39 system("wget -q -O %s %s%s" % (tempFile, args.url, entryId))
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40 tempSize = getsize(tempFile)
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41 if tempSize == 0:
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42 logFile.write("Entry `%s` not found.\n" % entryId)
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43 else:
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44 indexFile.write("%s\t%d\t%d\n" % (entryId, start, tempSize))
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45 start = start + tempSize + 1
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46 system("cat %s >> %s" % (tempFile, outputDatabase))
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47 logFile.flush()
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48 logFile.close()
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49
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50
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51 if __name__ == "__main__":
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52 parser = argparse.ArgumentParser(description='DBKit - Download and Merge files into a single file.')
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53 parser.add_argument('-l', '--list', help='List of entries', required=True)
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54 parser.add_argument('-u', '--url', help='Source Url', required=True)
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55 parser.add_argument('-t', '--temp', help='temp', required=True)
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56 parser.add_argument('-il', '--idlength', help='Format Identifier Length (integer)', required=False, default="0")
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57 parser.add_argument('-ic', '--idcase', help='Format Identifier Case (lower, upper)', required=False, default=None)
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58 parser.add_argument('-ie', '--idextension', help='Format Identifier Extension', required=False, default=None)
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59 parser.add_argument('-o', '--index', help='Output Database Index', required=True)
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60 parser.add_argument('-d', '--database', help='Output Database', required=True)
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61 parser.add_argument('-g', '--log', help="Log file", required=True)
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62 args = parser.parse_args()
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63 main(args)