Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/Reader.py @ 20:85971ec2a527 draft default tip

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 81d946d4544a4ea7e5b55f90caef971eca6abba0
author sargentl
date Fri, 21 Sep 2018 16:30:54 -0400
parents 43a700afd457
children
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
yating-l
parents: 6
diff changeset
1 import os
6
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2 import json
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
yating-l
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3 import shutil
6
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4 import logging
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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5 import codecs
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6
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7
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8 # Internal dependencies
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9 from datatypes.binary.Bam import Bam
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10 from datatypes.binary.BigWig import BigWig
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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11 from datatypes.interval.Bed import Bed
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12 from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats
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13 from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions
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14 from datatypes.interval.BlastXml import BlastXml
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15 from datatypes.interval.Gff3 import Gff3
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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16 from datatypes.interval.Gtf import Gtf
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17 from datatypes.interval.BigPsl import BigPsl
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18 from datatypes.interval.BedBlatAlignments import BedBlatAlignments
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19 from datatypes.interval.BedBlastAlignments import BedBlastAlignments
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20 from datatypes.interval.Psl import Psl
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21 from datatypes.sequence.Fasta import Fasta
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22 from util import santitizer
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23
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24 class Reader(object):
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25
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26 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats,
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27 BedSpliceJunctions, BigPsl, BedBlatAlignments, BedBlastAlignments,
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28 BlastXml, Gff3, Gtf, Psl, Fasta]
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29
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30 def __init__(self, input_json_file):
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31 self.inputFile = input_json_file
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32 self.args = self.loadJson()
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33
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34
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35 def loadJson(self):
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36 try:
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37 data_file = codecs.open(self.inputFile, 'r', 'utf-8')
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38 return json.load(data_file)
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39 except IOError:
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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40 print ("Cannot find JSON file\n")
6
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41 exit(1)
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42
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43 def getToolDir(self):
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44 try:
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45 return self.args["tool_directory"]
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46 except KeyError:
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47 print ("tool_directory is not defined in the input file!")
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48 exit(1)
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49
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50 def getExtFilesPath(self):
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51 try:
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52 return self.args["extra_files_path"]
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53 except KeyError:
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54 print ("extra_files_path is not defined in the input file!")
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55 exit(1)
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56
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57 def getUserEmail(self):
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58 try:
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59 return self.args["user_email"]
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60 except KeyError:
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61 print ("user_email is not defined in the input file!")
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62 exit(1)
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63
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64 def getDebugMode(self):
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65 try:
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66 return self.args["debug_mode"]
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67 except KeyError:
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68 print ("debug_mode is not defined in the input file!")
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69 exit(1)
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70
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71 def getTrackType(self):
7
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72 try:
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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73 return self.args.get("feature_tracks_type")
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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74 except KeyError:
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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75 print ("feature tracks type is not defined in the input file!")
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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76 exit(1)
6
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77
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78 def getGenomeName(self):
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79 genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
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80 return genome_name
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81
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82 def getRefGenome(self):
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83 array_inputs_reference_genome = self.args["fasta"]
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84 input_fasta_file = array_inputs_reference_genome["false_path"]
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85 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
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86 # Add "fasta" extension because Apollo needs it to create annotation
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87 refseq_file = os.path.join(os.path.dirname(input_fasta_file), input_fasta_file_name + ".fasta")
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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88 shutil.copyfile(input_fasta_file, refseq_file)
6
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89 genome_name = self.getGenomeName()
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90 reference_genome = Fasta(refseq_file,
6
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91 input_fasta_file_name, genome_name)
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92 return reference_genome
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93
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94 def getTracksData(self):
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95 self.logger = logging.getLogger(__name__)
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96 all_datatype_dictionary = dict()
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97 for datatype in self.DATATYPE_CLASS:
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98 class_name = datatype.__name__
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99 array_inputs = self.args.get(str(class_name))
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100 if array_inputs:
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101 self.logger.debug("Creating %s objects\n", class_name)
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102 self.logger.debug("array_inputs: %s", array_inputs)
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103 all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
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104
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105 return all_datatype_dictionary
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106
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107 def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
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108 """
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109 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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110 and update the dictionary of datatype
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111
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112 :param ExtensionClass:
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113 :param array_inputs:
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114 :type ExtensionClass: Datatype
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115 :type array_inputs: list[string]
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116 """
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117
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118 datatype_dictionary = {}
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119
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120 # TODO: Optimize this double loop
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121 for input_data in array_inputs:
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122 input_false_path = input_data["false_path"]
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123 # if the file is empty, skip the rest
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124 if os.path.isfile(input_false_path) and os.path.getsize(input_false_path) > 0:
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125 input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
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126 extensionObject = ExtensionClass(input_false_path, input_data)
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127 extensionObject.generateCustomTrack()
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128 datatype_dictionary.update({input_data["order_index"]: extensionObject})
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129 self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
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130 else:
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131 self.logger.info("The input file: %s is empty, skip creating the track for this data", input_data["name"])
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132 return datatype_dictionary
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133
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134
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135
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136
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137