comparison jbrowseArchiveCreator.py @ 25:31a41ce128cc draft

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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children 127037c49bc8
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24:bb6fdccef474 25:31a41ce128cc
1 #!/usr/bin/env python
2 # -*- coding: utf8 -*-
3
4 """
5 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
6 """
7
8 import sys
9 import argparse
10 import json
11 import logging
12 import collections
13
14
15 # Internal dependencies
16 from util.Reader import Reader
17 from util.Logger import Logger
18 from TrackHub import TrackHub
19
20
21 def main(argv):
22 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
23 parser.add_argument('-j', '--data_json', help='JSON file containing the metadata of the inputs')
24 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the JBrowse Hub Archive')
25
26 # Get the args passed in parameter
27 args = parser.parse_args()
28 json_inputs_data = args.data_json
29 outputFile = args.output
30
31 ##Parse JSON file with Reader
32 reader = Reader(json_inputs_data)
33
34 # Begin init variables
35 extra_files_path = reader.getExtFilesPath()
36 toolDirectory = reader.getToolDir()
37 #outputFile = reader.getOutputDir()
38 user_email = reader.getUserEmail()
39 reference_genome = reader.getRefGenome()
40 debug_mode = reader.getDebugMode()
41 track_type = reader.getTrackType()
42 #jbrowse_path = reader.getJBrowsePath()
43 apollo_host = reader.getApolloHost()
44 apollo_user = reader.getApolloUser()
45
46 #### Logging management ####
47 # If we are in Debug mode, also print in stdout the debug dump
48 log = Logger(tool_directory=toolDirectory, debug=debug_mode, extra_files_path=extra_files_path)
49 log.setup_logging()
50 logging.info('#### JBrowseArchiveCreator: Start ####\n')
51 logging.debug('---- Welcome in JBrowseArchiveCreator Debug Mode ----\n')
52 logging.debug('JSON parameters: %s\n\n', json.dumps(reader.args))
53 #### END Logging management ####
54
55 # Create the Track Hub folder
56 logging.info('#### JBrowseArchiveCreator: Creating the Track Hub folder ####\n')
57 trackHub = TrackHub(reference_genome, apollo_user, outputFile, extra_files_path, toolDirectory, track_type, apollo_host)
58
59 # Create Ordered Dictionary to add the tracks in the tool form order
60 logging.info('#### JBrowseArchiveCreator: Preparing track data ####\n')
61 all_datatype_dictionary = reader.getTracksData()
62 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
63
64 logging.debug("----- End of all_datatype_dictionary processing -----")
65 #logging.debug("all_datatype_ordered_dictionary are: %s", json.dumps(all_datatype_ordered_dictionary))
66
67 logging.info('#### JBrowseArchiveCreator: Adding tracks to Track Hub ####\n')
68 logging.debug("----- Beginning of Track adding processing -----")
69
70 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
71 trackHub.addTrack(datatypeObject.track.track_db)
72
73 logging.debug("----- End of Track adding processing -----")
74
75 # We terminate the process and so create a HTML file summarizing all the files
76 logging.info('#### JBrowseArchiveCreator: Creating the HTML file ####\n')
77 trackHub.terminate(debug_mode)
78
79 logging.debug('---- End of JBrowseArchiveCreator Debug Mode: Bye! ----\n')
80 logging.info('#### JBrowseArchiveCreator: Congratulation! Assembly Hub is created! ####\n')
81
82 sys.exit(0)
83
84 if __name__ == "__main__":
85 main(sys.argv)