Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/Reader.py @ 33:07cc5384dd61 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 74a020b6b0a2fa7ff5670d7f154de838dee51dfd
author yating-l
date Wed, 25 Oct 2017 12:43:23 -0400
parents 7b955a58d8f2
children 4a69515eed63
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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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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
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.Gtf import Gtf
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.BigPsl import BigPsl
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.BedBlatAlignments import BedBlatAlignments
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17 from datatypes.interval.BedBlastAlignments import BedBlastAlignments
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18 from datatypes.interval.Psl import Psl
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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19 from datatypes.sequence.Fasta import Fasta
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20 from util import santitizer
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22 class Reader(object):
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24 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats,
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25 BedSpliceJunctions, BigPsl, BedBlatAlignments, BedBlastAlignments,
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26 BlastXml, Gff3, Gtf, Psl, Fasta]
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28 def __init__(self, input_json_file):
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29 self.inputFile = input_json_file
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30 self.args = self.loadJson()
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33 def loadJson(self):
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34 try:
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35 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
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36 return json.load(data_file)
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37 except IOError:
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38 print "Cannot find JSON file\n"
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39 exit(1)
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41 def getToolDir(self):
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42 try:
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43 return self.args["tool_directory"]
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44 except KeyError:
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45 print ("tool_directory is not defined in the input file!")
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46 exit(1)
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48 def getExtFilesPath(self):
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49 try:
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50 return self.args["extra_files_path"]
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51 except KeyError:
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52 print ("extra_files_path is not defined in the input file!")
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53 exit(1)
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55 def getUserEmail(self):
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56 try:
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57 return self.args["user_email"]
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58 except KeyError:
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59 print ("user_email is not defined in the input file!")
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60 exit(1)
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62 def getDebugMode(self):
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63 try:
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64 return self.args["debug_mode"]
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65 except KeyError:
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66 print ("debug_mode is not defined in the input file!")
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67 exit(1)
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68
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69 def getTrackType(self):
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70 track_type = self.args.get("track_type")
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71 return track_type
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72
32
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73 def getGenomeName(self):
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74 genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
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75 return genome_name
25
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76
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77 def getRefGenome(self):
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78 array_inputs_reference_genome = self.args["fasta"]
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79 # TODO: Replace these with the object Fasta
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80 input_fasta_file = array_inputs_reference_genome["false_path"]
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81 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
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82 #genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
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83 genome_name = self.getGenomeName()
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84 reference_genome = Fasta(input_fasta_file,
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85 input_fasta_file_name, genome_name)
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86 return reference_genome
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87
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88 def getTracksData(self):
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89 self.logger = logging.getLogger(__name__)
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90 all_datatype_dictionary = dict()
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91 for datatype in self.DATATYPE_CLASS:
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92 class_name = datatype.__name__
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93 array_inputs = self.args.get(str(class_name))
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94 if array_inputs:
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95 self.logger.debug("Creating %s objects\n", class_name)
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96 self.logger.debug("array_inputs: %s", array_inputs)
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97 all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
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98
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99 return all_datatype_dictionary
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100
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101 def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
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102 """
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103 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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104 and update the dictionary of datatype
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105
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106 :param ExtensionClass:
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107 :param array_inputs:
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108 :type ExtensionClass: Datatype
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109 :type array_inputs: list[string]
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110 """
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111
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112 datatype_dictionary = {}
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113
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114 # TODO: Optimize this double loop
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115 for input_data in array_inputs:
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116 input_false_path = input_data["false_path"]
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117 input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
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118 extensionObject = ExtensionClass(input_false_path, input_data)
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119 extensionObject.generateCustomTrack()
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120 datatype_dictionary.update({input_data["order_index"]: extensionObject})
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121 self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
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122 return datatype_dictionary
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123
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124
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125
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126
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127