Mercurial > repos > yating-l > jbrowsearchivecreator
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 |
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date | Fri, 13 Oct 2017 12:44:31 -0400 |
parents | |
children | 127037c49bc8 |
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24:bb6fdccef474 | 25:31a41ce128cc |
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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) |