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annotate Gtf.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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3 import os
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4 import tempfile
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6 # Internal dependencies
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7 from Datatype import Datatype
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8 from util import subtools
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9
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10 class InfoModifiedGtf():
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11 def __init__(self, is_modified=False, array_modified_lines=[]):
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12 self.is_modified = is_modified
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13 self.array_modified_lines = array_modified_lines
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15 def get_str_modified_lines(self):
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16 return ','.join(map(str, self.array_modified_lines))
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18 class Gtf( Datatype ):
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19 def __init__( self, input_gtf_false_path, data_gtf):
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21 super(Gtf, self).__init__()
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23 self.track = None
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25 self.input_gtf_false_path = input_gtf_false_path
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26 self.name_gtf = data_gtf["name"]
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27 self.priority = data_gtf["order_index"]
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28 self.track_color = data_gtf["track_color"]
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29 # TODO: Think about how to avoid repetition of the group_name everywhere
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30 self.group_name = data_gtf["group_name"]
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32 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
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33
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34 # TODO: See if we need these temporary files as part of the generated files
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35 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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36 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
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37 sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred")
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38
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39 # GtfToGenePred
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40 ## Checking the integrity of the inputs
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41 modified_gtf = self._checkAndFixGtf()
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42
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43 ## Processing the gtf
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44 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
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45
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46 # TODO: From there, refactor because common use with Gff3.py
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47 # genePredToBigGenePred processing
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48 subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name)
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49
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50 # Sort processing
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51 subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name)
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52
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53 # bedToBigBed processing
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54 trackName = "".join( ( self.name_gtf, ".bb") )
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55
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56 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
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57
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58 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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59
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60 with open(myBigBedFilePath, 'w') as bigBedFile:
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61 subtools.bedToBigBed(sorted_bigGenePred_file.name,
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62 self.chromSizesFile.name,
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63 bigBedFile.name,
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64 autoSql=auto_sql_option,
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65 typeOption='bed12+8',
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66 tab=True)
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67
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68
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69 # Create the Track Object
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70 self.createTrack(file_path=trackName,
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71 track_name=trackName,
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72 long_label=self.name_gtf, track_type='bigGenePred',
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73 visibility='dense', priority=self.priority,
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74 track_file=myBigBedFilePath,
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75 track_color=self.track_color,
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76 group_name=self.group_name)
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77
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78 # TODO: Use Logging instead of print
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79 if modified_gtf.is_modified:
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80 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues."
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81 % self.name_gtf)
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82 print("Here are the lines removed: " + modified_gtf.get_str_modified_lines())
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83 else:
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84 print("- Gtf %s created" % self.name_gtf)
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85
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86 def _checkAndFixGtf(self):
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87 """
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88 Call _checkAndFixGtf, check the integrity of gtf file,
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89 if coordinates exceed chromosome size, either removed the whole line(s) or truncated to the end of the scaffold
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90 depending on the user choice
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91 default: remove the whole line(s)
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92 """
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93 # Set the boolean telling if we had to modify the file
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94 modified_gtf = InfoModifiedGtf()
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95
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96 # Create a temp gtf just in case we have issues
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97 temp_gtf = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gtf", delete=False)
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98
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99 # TODO: Get the user choice and use it
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100 # TODO: Check if the start > 0 and the end <= chromosome size
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101 # Get the chrom.sizes into a dictionary to have a faster access
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102 # TODO: Think about doing this in Datatype.py, so everywhere we have access to this read-only dictionary
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103 dict_chrom_sizes = {}
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104 with open(self.chromSizesFile.name, 'r') as chromSizes:
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105 lines = chromSizes.readlines()
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106 for line in lines:
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107 fields = line.split()
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108 # fields[1] should be the name of the scaffold
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109 # fields[2] should be the size of the scaffold
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110 # TODO: Ensure this is true for all lines
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111 dict_chrom_sizes[fields[0]] = fields[1]
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112
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113 # Parse the GTF and check each line using the chrom sizes dictionary
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114 with open(temp_gtf.name, 'a+') as tmp:
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115 with open(self.input_gtf_false_path, 'r') as gtf:
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116 lines = gtf.readlines()
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117 for index, line in enumerate(lines):
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118 # If this is not a comment, we check the fields
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119 if not line.startswith('#'):
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120 fields = line.split()
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121 # We are interested in fields[0] => Seqname (scaffold)
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122 # We are interested in fields[3] => Start of the scaffold
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123 # We are interested in fields[4] => End of the scaffold
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124 scaffold_size = dict_chrom_sizes[fields[0]]
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125 start_position = fields[3]
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126 end_position = fields[4]
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127
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128 if start_position > 0 and end_position <= scaffold_size:
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129 # We are good, so we copy this line
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130 tmp.write(line)
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131 tmp.write(os.linesep)
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132
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133
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134 # The sequence is not good, we are going to process it regarding the user choice
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135 # TODO: Process the user choice
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136 # By default, we are assuming the user choice is to remove the lines: We don't copy it
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137
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138 # If we are here, it means the gtf has been modified
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139 else:
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140 # We save the line for the feedback to the user
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141 modified_gtf.array_modified_lines.append(index + 1)
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142
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143 if modified_gtf.is_modified is False:
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144 modified_gtf.is_modified = True
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145 else:
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146 pass
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147 else:
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148 tmp.write(line)
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149 tmp.write(os.linesep)
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150
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151 # Once the process it completed, we just replace the path of the gtf
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152 self.input_gtf_false_path = temp_gtf.name
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153
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154 # TODO: Manage the issue with the fact the dataset is going to still exist on the disk because of delete=False
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155
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156 return modified_gtf