Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/index/TrixIndex.py @ 25:31a41ce128cc draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
author yating-l
date Fri, 13 Oct 2017 12:44:31 -0400
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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1 #!/usr/bin/python
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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3 import os
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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4 import collections
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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5 import shutil
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6 import logging
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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7 from ExternIndex import ExternIndex
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9 class TrixIndex(ExternIndex):
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10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
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11 self.logger = logging.getLogger(__name__)
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12 self.indexIx = indexIx
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13 self.indexIxx = indexIxx
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14 self.trackName = trackName
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15 self.mySpecieFolderPath = mySpecieFolderPath
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16 self.trixId = trixId.strip()
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17 if not self.trixId:
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18 self.logger.error("Didn't specify the Trix identifier. To use TRIX index, you need to specify the identifier")
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19 exit(1)
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20 if "default_index" in args:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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21 self.default_index = args["default_index"]
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22 else:
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23 self.default_index = None
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24 self.index_settings = collections.OrderedDict()
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26 def setExtLink(self):
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27 self.setSearchIndex()
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28 self.moveIndexFile()
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29 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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30 return self.index_settings
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32 def moveIndexFile(self):
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33 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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34 self.indexIxName = "".join( ( self.trackName, ".ix") )
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35 self.indexIxxName = "".join( ( self.trackName, ".ixx") )
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36 if not os.path.exists(indexFolder):
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37 os.makedirs(indexFolder)
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39 # Move index files to the index folder
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40 self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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41 shutil.copyfile(self.indexIx, self.indexIxPath)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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42 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
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43 shutil.copyfile(self.indexIxx, self.indexIxxPath)
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45 def setSearchIndex(self):
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46 if self.default_index:
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47 set_index = set()
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48 set_index.add(self.trixId)
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49 set_index.add(self.default_index)
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50 search_index = ",".join(set_index)
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51 else:
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52 search_index = self.trixId
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53 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
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54 self.index_settings["searchIndex"] = search_index
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