Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/Reader.py @ 31:127037c49bc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
author yating-l
date Mon, 16 Oct 2017 18:03:58 -0400
parents 31a41ce128cc
children 7b955a58d8f2
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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1 import json
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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2 import logging
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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3 import codecs
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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4
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5
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6 # Internal dependencies
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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7 from datatypes.binary.Bam import Bam
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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8 from datatypes.binary.BigWig import BigWig
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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9 from datatypes.interval.Bed import Bed
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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10 from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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11 from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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12 from datatypes.interval.BlastXml import BlastXml
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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13 from datatypes.interval.Gff3 import Gff3
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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14 from datatypes.interval.Gff3_mrna import Gff3_mrna
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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15 from datatypes.interval.Gff3_transcript import Gff3_transcript
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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16 from datatypes.interval.Gtf import Gtf
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17 from datatypes.interval.GtfStringTie import GtfStringTie
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18 from datatypes.interval.BigPsl import BigPsl
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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19 from datatypes.interval.BedBlatAlignments import BedBlatAlignments
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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20 from datatypes.interval.BedBlastAlignments import BedBlastAlignments
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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21 from datatypes.interval.Psl import Psl
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22 from datatypes.sequence.Fasta import Fasta
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23 from apollo.ApolloUser import ApolloUser
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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24 from util import santitizer
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26 class Reader(object):
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28 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats,
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29 BedSpliceJunctions, BigPsl, BedBlatAlignments, BedBlastAlignments,
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30 BlastXml, Gff3, Gff3_mrna, Gff3_transcript, Gff3_mrna, Gtf, GtfStringTie, Psl, Fasta]
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31
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32 def __init__(self, input_json_file):
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33 self.inputFile = input_json_file
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34 self.args = self.loadJson()
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36
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37 def loadJson(self):
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38 try:
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39 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
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40 return json.load(data_file)
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41 except IOError:
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42 print "Cannot find JSON file\n"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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43 exit(1)
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44
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45 def getToolDir(self):
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46 try:
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47 return self.args["tool_directory"]
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48 except KeyError:
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49 print ("tool_directory is not defined in the input file!")
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50 exit(1)
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51
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52 def getExtFilesPath(self):
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53 try:
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54 return self.args["extra_files_path"]
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55 except KeyError:
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56 print ("extra_files_path is not defined in the input file!")
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57 exit(1)
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58
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59 def getUserEmail(self):
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60 try:
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61 return self.args["user_email"]
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62 except KeyError:
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63 print ("user_email is not defined in the input file!")
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64 exit(1)
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65
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66 def getDebugMode(self):
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67 try:
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68 return self.args["debug_mode"]
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69 except KeyError:
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70 print ("debug_mode is not defined in the input file!")
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71 exit(1)
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72
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73 def getTrackType(self):
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74 track_type = self.args.get("track_type")
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75 return track_type
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76
31
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77 def getApolloPath(self):
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78 apollo_path = self.args.get("apollo_path")
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79 return apollo_path
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80
25
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81 def getApolloHost(self):
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82 apollo_host = self.args.get("apollo_host")
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83 return apollo_host
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84
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85
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86 def getRefGenome(self):
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87 array_inputs_reference_genome = self.args["fasta"]
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88 # TODO: Replace these with the object Fasta
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89 input_fasta_file = array_inputs_reference_genome["false_path"]
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90 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
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91 genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
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92 reference_genome = Fasta(input_fasta_file,
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93 input_fasta_file_name, genome_name)
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94 return reference_genome
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95
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96 def getApolloUser(self):
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97 user_info = self.args.get("apollo_user")
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98 if not user_info:
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99 firstname = "demo"
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100 lastname = "user"
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101 password = "gonramp"
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102 user_email = self.getUserEmail()
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103 else:
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104 firstname = user_info['firstname']
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105 lastname = user_info['lastname']
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106 user_email = user_info['user_email']
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107 password = user_info['password']
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108 apollo_user = ApolloUser(user_email, firstname, lastname, password)
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109 return apollo_user
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110
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111 def getTracksData(self):
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112 self.logger = logging.getLogger(__name__)
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113 all_datatype_dictionary = dict()
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114 for datatype in self.DATATYPE_CLASS:
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115 class_name = datatype.__name__
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116 array_inputs = self.args.get(str(class_name))
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117 if array_inputs:
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118 self.logger.debug("Creating %s objects\n", class_name)
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119 self.logger.debug("array_inputs: %s", array_inputs)
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120 all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
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121
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122 return all_datatype_dictionary
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123
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124 def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
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125 """
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126 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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127 and update the dictionary of datatype
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128
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129 :param ExtensionClass:
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130 :param array_inputs:
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131 :type ExtensionClass: Datatype
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132 :type array_inputs: list[string]
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133 """
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134
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135 datatype_dictionary = {}
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136
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137 # TODO: Optimize this double loop
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138 for input_data in array_inputs:
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139 input_false_path = input_data["false_path"]
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140 input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
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141 extensionObject = ExtensionClass(input_false_path, input_data)
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142 extensionObject.generateCustomTrack()
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143 datatype_dictionary.update({input_data["order_index"]: extensionObject})
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144 self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
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145 return datatype_dictionary
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146
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147
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148
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149
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150