Mercurial > repos > yating-l > hubarchivecreatortest

annotate hubArchiveCreator.py @ 1:85195e0d4b71 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
author yating-l
date Fri, 29 Sep 2017 13:32:23 -0400
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """
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5 This Galaxy tool permits to prepare your files to be ready for
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6 Assembly Hub visualization.
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7 Program test arguments:
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8 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f '{"false_path": "./test-data/common/dbia3.fa", "name":"dbia3"}' -d . -u ./tools -o output.html
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9 """
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11 import argparse
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12 import collections
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13 import json
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14 import logging
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15 import os
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16 import sys
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18 # Internal dependencies
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19 from util.Reader import Reader
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20 from util.Logger import Logger
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21 from TrackHub import TrackHub
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25 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
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28 def main(argv):
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30 # Command Line parsing init
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31 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
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32 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
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33 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')
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35 # Get the args passed in parameter
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36 args = parser.parse_args()
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37 json_inputs_data = args.data_json
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38 outputFile = args.output
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40 ##Parse JSON file with Reader
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41 reader = Reader(json_inputs_data)
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43 # Begin init variables
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44 extra_files_path = reader.getExtFilesPath()
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45 toolDirectory = reader.getToolDir()
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46 #outputFile = reader.getOutputDir()
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47 user_email = reader.getUserEmail()
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48 reference_genome = reader.getRefGenome()
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49 debug_mode = reader.getDebugMode()
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51 #### Logging management ####
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52 # If we are in Debug mode, also print in stdout the debug dump
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53 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
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54 log.setup_logging()
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55 logging.info('#### HubArchiveCreator: Start ####\n')
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56 logging.debug('---- Welcome in HubArchiveCreator Debug Mode ----\n')
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57 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
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58 #### END Logging management ####
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60 # Create the Track Hub folder
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61 logging.info('#### HubArchiveCreator: Creating the Track Hub folder ####\n')
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62 trackHub = TrackHub(reference_genome, user_email, outputFile, extra_files_path, toolDirectory)
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64 # Create Ordered Dictionary to add the tracks in the tool form order
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65 logging.info('#### HubArchiveCreator: Preparing track data ####\n')
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66 all_datatype_dictionary = reader.getTracksData()
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67 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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69 logging.debug("----- End of all_datatype_dictionary processing -----")
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70 #logging.debug("all_datatype_ordered_dictionary are: %s", json.dumps(all_datatype_ordered_dictionary))
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72 logging.info('#### HubArchiveCreator: Adding tracks to Track Hub ####\n')
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73 logging.debug("----- Beginning of Track adding processing -----")
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75 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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76 trackHub.addTrack(datatypeObject.track.track_db)
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78 logging.debug("----- End of Track adding processing -----")
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80 # We terminate the process and so create a HTML file summarizing all the files
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81 logging.info('#### HubArchiveCreator: Creating the HTML file ####\n')
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82 trackHub.terminate()
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84 logging.debug('---- End of HubArchiveCreator Debug Mode: Bye! ----\n')
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85 logging.info('#### HubArchiveCreator: Congratulation! Assembly Hub is created! ####\n')
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87 sys.exit(0)
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89 if __name__ == "__main__":
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90 main(sys.argv)