Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowseArchiveCreator.py @ 31:127037c49bc8 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 Mon, 16 Oct 2017 18:03:58 -0400
parents 31a41ce128cc
children 7b955a58d8f2
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1 #!/usr/bin/env python
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2 # -*- coding: utf8 -*-
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4 """
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5 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
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6 """
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8 import sys
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9 import argparse
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10 import json
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11 import logging
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12 import collections
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15 # Internal dependencies
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16 from util.Reader import Reader
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17 from util.Logger import Logger
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18 from TrackHub import TrackHub
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21 def main(argv):
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22 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
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23 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
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24 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the JBrowse Hub Archive')
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26 # Get the args passed in parameter
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27 args = parser.parse_args()
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28 json_inputs_data = args.data_json
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29 outputFile = args.output
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31 ##Parse JSON file with Reader
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32 reader = Reader(json_inputs_data)
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34 # Begin init variables
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35 extra_files_path = reader.getExtFilesPath()
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36 toolDirectory = reader.getToolDir()
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37 #outputFile = reader.getOutputDir()
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38 user_email = reader.getUserEmail()
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39 reference_genome = reader.getRefGenome()
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40 debug_mode = reader.getDebugMode()
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41 track_type = reader.getTrackType()
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42 #jbrowse_path = reader.getJBrowsePath()
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43 apollo_path = reader.getApolloPath()
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44 apollo_host = reader.getApolloHost()
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45 apollo_user = reader.getApolloUser()
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47 #### Logging management ####
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48 # If we are in Debug mode, also print in stdout the debug dump
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49 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
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50 log.setup_logging()
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51 logging.info('#### JBrowseArchiveCreator: Start ####\n')
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52 logging.debug('---- Welcome in JBrowseArchiveCreator Debug Mode ----\n')
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53 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
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54 #### END Logging management ####
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56 # Create the Track Hub folder
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57 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
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58 trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host, user_email)
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60 # Create Ordered Dictionary to add the tracks in the tool form order
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61 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')
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62 all_datatype_dictionary = reader.getTracksData()
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63 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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65 logging.debug("----- End of all_datatype_dictionary processing -----")
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66 #logging.debug("all_datatype_ordered_dictionary are: %s", json.dumps(all_datatype_ordered_dictionary))
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68 logging.info('#### JBrowseArchiveCreator: Adding tracks to Track Hub ####\n')
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69 logging.debug("----- Beginning of Track adding processing -----")
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71 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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72 trackHub.addTrack(datatypeObject.track.track_db)
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74 logging.debug("----- End of Track adding processing -----")
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76 # We terminate the process and so create a HTML file summarizing all the files
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77 logging.info('#### JBrowseArchiveCreator: Creating the HTML file ####\n')
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78 trackHub.terminate(debug_mode)
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80 logging.debug('---- End of JBrowseArchiveCreator Debug Mode: Bye! ----\n')
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81 logging.info('#### JBrowseArchiveCreator: Congratulation! Assembly Hub is created! ####\n')
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83 sys.exit(0)
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85 if __name__ == "__main__":
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86 main(sys.argv)