Mercurial > repos > yating-l > jbrowsearchivecreator

comparison util/Reader.py @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
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children 5d5fdcb798da
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5:e762f4b9e4bd 6:237707a6b74d
1 import json
2 import logging
3 import codecs
4
5
6 # Internal dependencies
7 from datatypes.binary.Bam import Bam
8 from datatypes.binary.BigWig import BigWig
9 from datatypes.interval.Bed import Bed
10 from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats
11 from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions
12 from datatypes.interval.BlastXml import BlastXml
13 from datatypes.interval.Gff3 import Gff3
14 from datatypes.interval.Gtf import Gtf
15 from datatypes.interval.BigPsl import BigPsl
16 from datatypes.interval.BedBlatAlignments import BedBlatAlignments
17 from datatypes.interval.BedBlastAlignments import BedBlastAlignments
18 from datatypes.interval.Psl import Psl
19 from datatypes.sequence.Fasta import Fasta
20 from util import santitizer
21
22 class Reader(object):
23
24 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats,
25 BedSpliceJunctions, BigPsl, BedBlatAlignments, BedBlastAlignments,
26 BlastXml, Gff3, Gtf, Psl, Fasta]
27
28 def __init__(self, input_json_file):
29 self.inputFile = input_json_file
30 self.args = self.loadJson()
31
32
33 def loadJson(self):
34 try:
35 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
36 return json.load(data_file)
37 except IOError:
38 print "Cannot find JSON file\n"
39 exit(1)
40
41 def getToolDir(self):
42 try:
43 return self.args["tool_directory"]
44 except KeyError:
45 print ("tool_directory is not defined in the input file!")
46 exit(1)
47
48 def getExtFilesPath(self):
49 try:
50 return self.args["extra_files_path"]
51 except KeyError:
52 print ("extra_files_path is not defined in the input file!")
53 exit(1)
54
55 def getUserEmail(self):
56 try:
57 return self.args["user_email"]
58 except KeyError:
59 print ("user_email is not defined in the input file!")
60 exit(1)
61
62 def getDebugMode(self):
63 try:
64 return self.args["debug_mode"]
65 except KeyError:
66 print ("debug_mode is not defined in the input file!")
67 exit(1)
68
69 def getTrackType(self):
70 track_type = self.args.get("track_type")
71 return track_type
72
73 def getGenomeName(self):
74 genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
75 return genome_name
76
77 def getRefGenome(self):
78 array_inputs_reference_genome = self.args["fasta"]
79 # TODO: Replace these with the object Fasta
80 input_fasta_file = array_inputs_reference_genome["false_path"]
81 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
82 #genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
83 genome_name = self.getGenomeName()
84 reference_genome = Fasta(input_fasta_file,
85 input_fasta_file_name, genome_name)
86 return reference_genome
87
88 def getTracksData(self):
89 self.logger = logging.getLogger(__name__)
90 all_datatype_dictionary = dict()
91 for datatype in self.DATATYPE_CLASS:
92 class_name = datatype.__name__
93 array_inputs = self.args.get(str(class_name))
94 if array_inputs:
95 self.logger.debug("Creating %s objects\n", class_name)
96 self.logger.debug("array_inputs: %s", array_inputs)
97 all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
98
99 return all_datatype_dictionary
100
101 def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
102 """
103 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
104 and update the dictionary of datatype
105
106 :param ExtensionClass:
107 :param array_inputs:
108 :type ExtensionClass: Datatype
109 :type array_inputs: list[string]
110 """
111
112 datatype_dictionary = {}
113
114 # TODO: Optimize this double loop
115 for input_data in array_inputs:
116 input_false_path = input_data["false_path"]
117 input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
118 extensionObject = ExtensionClass(input_false_path, input_data)
119 extensionObject.generateCustomTrack()
120 datatype_dictionary.update({input_data["order_index"]: extensionObject})
121 self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
122 return datatype_dictionary
123
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