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annotate Datatype.py @ 0:0bca8a6364a7 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 17:21:18 -0500
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """
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5 Super Class of the managed datatype
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6 """
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8 import os
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9 import tempfile
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11 from util import subtools
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12 from Track import Track
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13 from TrackDb import TrackDb
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16 class Datatype(object):
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18 twoBitFile = None
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20 input_fasta_file = None
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21 extra_files_path = None
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22 tool_directory = None
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24 mySpecieFolderPath = None
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25 myTrackFolderPath = None
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27 twoBitFile = None
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28 chromSizesFile = None
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30 track = None
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32 def __init__(self):
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33
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34 not_init_message = "The {0} is not initialized." \
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35 "Did you use pre_init static method first?"
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36 if Datatype.input_fasta_file is None:
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37 raise TypeError(not_init_message.format('reference genome'))
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38 if Datatype.extra_files_path is None:
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39 raise TypeError(not_init_message.format('track Hub path'))
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40 if Datatype.tool_directory is None:
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41 raise TypeError(not_init_message.format('tool directory'))
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43 @staticmethod
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44 def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
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45 extra_files_path, tool_directory, specie_folder, tracks_folder):
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46 Datatype.extra_files_path = extra_files_path
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47 Datatype.tool_directory = tool_directory
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48
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49 # TODO: All this should be in TrackHub and not in Datatype
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50 Datatype.mySpecieFolderPath = specie_folder
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51 Datatype.myTrackFolderPath = tracks_folder
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52
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53 Datatype.input_fasta_file = reference_genome
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54
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55 # 2bit file creation from input fasta
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56 Datatype.twoBitFile = two_bit_path
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57 Datatype.chromSizesFile = chrom_sizes_file
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58
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59 @staticmethod
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60 def get_largest_scaffold_name(self):
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61 # We can get the biggest scaffold here, with chromSizesFile
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62 with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
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63 # TODO: Check if exists
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64 return chrom_sizes.readline().split()[0]
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65
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66 # TODO: Rename for PEP8
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67 def getShortName( self, name_to_shortify ):
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68 # Slice to get from Long label the short label
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69 short_label_slice = slice(0, 15)
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70
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71 return name_to_shortify[short_label_slice]
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72
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73 # TODO: Better handle parameters, use heritance mecanism
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74 # TODO: Use default parameters for some, like visibility
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75 def createTrack(self,
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76 file_path=None,
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77 track_name=None, long_label=None, thick_draw_item='off',
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78 short_label=None, track_type=None, visibility=None, priority=None,
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79 track_file=None, track_color='#000000', group_name="Default"):
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80
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81 # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
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82 data_url = "tracks/%s" % file_path
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83
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84 if not short_label:
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85 short_label = self.getShortName(long_label)
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86
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87 # Replace '_' by ' ', to invert the sanitization mecanism
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88 # TODO: Find a better way to manage the sanitization of file path
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89 long_label = long_label.replace("_", " ")
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90 short_label = short_label.replace("_", " ")
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91
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92 #TODO: Check if rgb or hexa
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93 # Convert hexa to rgb array
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94 hexa_without_sharp = track_color.lstrip('#')
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95 rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
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96 rgb_ucsc = ','.join(map(str, rgb_array))
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97
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98 track_db = TrackDb(
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99 trackName=track_name,
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100 longLabel=long_label,
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101 shortLabel=short_label,
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102 trackDataURL=data_url,
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103 trackType=track_type,
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104 visibility=visibility,
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105 thickDrawItem=thick_draw_item,
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106 priority=priority,
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107 track_color=rgb_ucsc,
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108 group_name=group_name
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109 )
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110
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111 # Return the Bam Track Object
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112 self.track = Track(
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113 trackFile=track_file,
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114 trackDb=track_db,
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115 )