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