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18
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1 #!/usr/bin/env python
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2
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3 import re
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4 from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
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5
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6 class removeDescriptionInFastaHeaderProgramLauncher(AbstractProgramLauncher):
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7
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8 def __init__( self ):
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9 AbstractProgramLauncher.__init__( self )
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10 self._formatInFile = "fasta"
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11
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12 def run( self ):
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13 self.checkInput()
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14 fastaHandler = open(self.getInputFile(), "r")
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15 lines = fastaHandler.readlines()
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16 fastaHandler.close()
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17 newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"])
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18
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19 self._writePreprocessedFastaFile(lines, newFastaName)
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20
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21 def _writePreprocessedFastaFile(self, lines, newFastaName):
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22 newFastaHandler = open(newFastaName, "w")
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23 for line in lines:
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24 if re.match(">", line):
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25 newLine = line.split(" ",1)[0] + "\n"
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26 newFastaHandler.write(newLine)
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27 else:
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28 newFastaHandler.write(line)
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29 newFastaHandler.close()
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30
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31
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32
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33
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34 if __name__ == "__main__":
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35 i = removeDescriptionInFastaHeaderProgramLauncher()
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36 i.checkAttributesFromCmdLine()
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37 i.run()
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