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annotate Gff3.py @ 24:fcc1021bd496 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author yating-l
date Wed, 31 May 2017 11:35:16 -0400
parents 2677f1899aa8
children df42241d3731
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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 Track import Track
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9 from TrackDb import TrackDb
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10 from util import subtools
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13 class Gff3( Datatype ):
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14 def __init__(self, input_Gff3_false_path, data_gff3):
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15 super( Gff3, self ).__init__()
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17 self.track = None
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19 self.input_Gff3_false_path = input_Gff3_false_path
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20 self.name_gff3 = data_gff3["name"]
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21 self.priority = data_gff3["order_index"]
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22 self.track_color = data_gff3["track_color"]
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23 # TODO: Think about how to avoid repetition of the group_name everywhere
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24 self.group_name = data_gff3["group_name"]
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25 if data_gff3["long_label"]:
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26 self.long_label = data_gff3["long_label"]
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27 else:
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28 self.long_label = self.name_gff3
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29 # TODO: See if we need these temporary files as part of the generated files
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30 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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31 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
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32 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
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34 # gff3ToGenePred processing
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35 subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
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37 # genePredToBigGenePred
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38 subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
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40 # Sort processing
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41 subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
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43 # TODO: Check if no errors
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45 # bedToBigBed processing
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46 trackName = "".join( (self.name_gff3, ".bb" ) )
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48 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
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49
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50 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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52 with open(myBigBedFilePath, 'w') as bigBedFile:
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53 subtools.bedToBigBed(sorted_biGenePred_file.name,
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54 self.chromSizesFile.name,
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55 bigBedFile.name,
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56 autoSql=auto_sql_option,
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57 typeOption='bed12+8',
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58 tab=True)
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60 # Create the Track Object
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61 self.createTrack(file_path=trackName,
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62 track_name=trackName,
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63 long_label=self.long_label,
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64 track_type='bigGenePred', visibility='dense',
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65 priority=self.priority,
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66 track_file=myBigBedFilePath,
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67 track_color=self.track_color,
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68 group_name=self.group_name)
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69
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70 print("- Gff3 %s created" % self.name_gff3)