Mercurial > repos > guerler > dbkit

annotate dbkit_package/DBKit.py @ 5:184b00847620 draft default tip

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"planemo upload commit 49504c53e0cdd7b98908b064fad4c0b8baeaa317"
author guerler
date Thu, 11 Mar 2021 19:31:37 +0000
parents 03e124ff7e26
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 from os.path import isfile, getsize
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4 class DBKit:
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5 def __init__(self, indexFile, databaseFile):
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6 self.databaseFile = databaseFile
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7 self.index = dict()
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8 with open(indexFile) as file:
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9 for line in file:
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10 cols = line.split()
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11 try:
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12 identifier = cols[0]
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13 start = int(cols[1])
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14 size = int(cols[2])
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15 self.index[identifier] = [start, size]
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16 except Exception:
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17 raise Exception("Invalid DBKit Index file format: %s." % line)
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18
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19 def createFile(self, identifier, outputName):
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20 if identifier in self.index:
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21 entry = self.index[identifier]
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22 start = entry[0]
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23 size = entry[1]
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24 with open(self.databaseFile) as file:
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25 file.seek(start)
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26 content = file.read(size)
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27 outputFile = open(outputName, "w")
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28 outputFile.write(content)
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29 outputFile.close()
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30 return True
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31 else:
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32 return False
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33
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34 def getIndex(self):
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35 return self.index
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37
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38 def writeEntry(identifier, fileName, outputIndex, outputDatabase):
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39 if isfile(outputDatabase):
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40 currentSize = getsize(outputDatabase)
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41 else:
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42 currentSize = 0
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43 if isfile(fileName):
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44 entrySize = getsize(fileName)
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45 else:
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46 entrySize = 0
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47 if entrySize > 0:
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48 outputIndexFile = open(outputIndex, "a+")
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49 outputIndexFile.write("%s\t%s\t%s\n" % (identifier, currentSize, entrySize))
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50 tempFile = open(fileName, "r")
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51 databaseFile = open(outputDatabase, "a+")
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52 databaseFile.write(tempFile.read())
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53 databaseFile.close()
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54 tempFile.close()
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55 outputIndexFile.close()
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56 return True
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57 else:
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58 return False