Mercurial > repos > rmarenco > hubarchivecreator

annotate Gtf.py @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 2677f1899aa8
children
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rmarenco
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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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14
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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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31 self.database = data_gtf["database"]
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32 if data_gtf["long_label"]:
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33 self.long_label = data_gtf["long_label"]
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34 else:
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35 self.long_label = self.name_gtf
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36 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
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38 # TODO: See if we need these temporary files as part of the generated files
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39 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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40 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
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41 sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred")
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43 # GtfToGenePred
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44 ## Checking the integrity of the inputs
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45 modified_gtf = self._checkAndFixGtf()
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46
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47 ## Processing the gtf
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48 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
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50 # TODO: From there, refactor because common use with Gff3.py
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51 # genePredToBigGenePred processing
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52 subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name)
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54 # Sort processing
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55 subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name)
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57 # bedToBigBed processing
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58 trackName = "".join( ( self.name_gtf, ".bb") )
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60 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
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61
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62 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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63
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64 with open(myBigBedFilePath, 'w') as bigBedFile:
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65 subtools.bedToBigBed(sorted_bigGenePred_file.name,
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66 self.chromSizesFile.name,
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67 bigBedFile.name,
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68 autoSql=auto_sql_option,
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69 typeOption='bed12+8',
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70 tab=True,
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71 extraIndex='name')
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72
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74 # Create the Track Object
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75 self.createTrack(file_path=trackName,
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76 track_name=trackName,
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77 long_label=self.long_label, track_type='bigGenePred',
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78 visibility='dense', priority=self.priority,
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79 track_file=myBigBedFilePath,
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80 track_color=self.track_color,
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81 group_name=self.group_name,
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82 database=self.database)
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83
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84 # TODO: Use Logging instead of print
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85 if modified_gtf.is_modified:
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86 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues."
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87 % self.name_gtf)
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88 print("Here are the lines removed: " + modified_gtf.get_str_modified_lines())
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89 else:
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90 print("- Gtf %s created" % self.name_gtf)
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91
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92 def _checkAndFixGtf(self):
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93 """
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94 Call _checkAndFixGtf, check the integrity of gtf file,
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95 if coordinates exceed chromosome size, either removed the whole line(s) or truncated to the end of the scaffold
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96 depending on the user choice
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97 default: remove the whole line(s)
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98 """
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99 # Set the boolean telling if we had to modify the file
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100 modified_gtf = InfoModifiedGtf()
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101
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102 # Create a temp gtf just in case we have issues
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103 temp_gtf = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gtf", delete=False)
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104
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105 # TODO: Get the user choice and use it
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106 # TODO: Check if the start > 0 and the end <= chromosome size
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107 # Get the chrom.sizes into a dictionary to have a faster access
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108 # TODO: Think about doing this in Datatype.py, so everywhere we have access to this read-only dictionary
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109 dict_chrom_sizes = {}
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110 with open(self.chromSizesFile.name, 'r') as chromSizes:
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111 lines = chromSizes.readlines()
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112 for line in lines:
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113 fields = line.split()
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114 # fields[1] should be the name of the scaffold
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115 # fields[2] should be the size of the scaffold
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116 # TODO: Ensure this is true for all lines
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117 dict_chrom_sizes[fields[0]] = fields[1]
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118
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119 # Parse the GTF and check each line using the chrom sizes dictionary
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120 with open(temp_gtf.name, 'a+') as tmp:
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121 with open(self.input_gtf_false_path, 'r') as gtf:
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122 lines = gtf.readlines()
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123 for index, line in enumerate(lines):
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124 # If this is not a comment, we check the fields
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125 if not line.startswith('#'):
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126 fields = line.split()
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127 # We are interested in fields[0] => Seqname (scaffold)
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128 # We are interested in fields[3] => Start of the scaffold
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129 # We are interested in fields[4] => End of the scaffold
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130 scaffold_size = dict_chrom_sizes[fields[0]]
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131 start_position = fields[3]
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132 end_position = fields[4]
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133
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134 if start_position > 0 and end_position <= scaffold_size:
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135 # We are good, so we copy this line
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136 tmp.write(line)
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137 tmp.write(os.linesep)
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138
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139
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140 # The sequence is not good, we are going to process it regarding the user choice
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141 # TODO: Process the user choice
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142 # By default, we are assuming the user choice is to remove the lines: We don't copy it
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143
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144 # If we are here, it means the gtf has been modified
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145 else:
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146 # We save the line for the feedback to the user
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147 modified_gtf.array_modified_lines.append(index + 1)
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148
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149 if modified_gtf.is_modified is False:
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150 modified_gtf.is_modified = True
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151 else:
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152 pass
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153 else:
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154 tmp.write(line)
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155 tmp.write(os.linesep)
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156
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157 # Once the process it completed, we just replace the path of the gtf
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158 self.input_gtf_false_path = temp_gtf.name
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159
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160 # 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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161
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162 return modified_gtf