Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/cleaning/TranscriptListCleaner.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 import sys
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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31 from SMART.Java.Python.structure.TranscriptList import TranscriptList
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 from SMART.Java.Python.misc.Progress import Progress
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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34
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 class TranscriptListCleaner(object):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 """A (quite generic) class that cleans a file containing transcripts"""
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37
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38 def __init__(self, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 self.verbosity = verbosity
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40
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41 def setInputFileName(self, fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 try:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 self.inputHandle = open(fileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 except IOError:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
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46
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47 def setOutputFileName(self, fileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 try:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 self.outputHandle = open(fileName, "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 except IOError:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
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52
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53 def getFileFormats():
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54 pass
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55 getFileFormats = staticmethod(getFileFormats)
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56
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57 def close(self):
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58 self.inputHandle.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 self.outputHandle.close()
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60
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61 def clean(self):
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62 self._clean()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 self.close()