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annotate Gff3.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 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 self.database = data_gff3["database"]
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26 if data_gff3["long_label"]:
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27 self.long_label = data_gff3["long_label"]
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28 else:
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29 self.long_label = self.name_gff3
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30 # TODO: See if we need these temporary files as part of the generated files
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31 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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32 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
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33 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
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35 # gff3ToGenePred processing
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36 subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
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38 # genePredToBigGenePred
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39 subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
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41 # Sort processing
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42 subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
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44 # TODO: Check if no errors
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46 # bedToBigBed processing
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47 trackName = "".join( (self.name_gff3, ".bb" ) )
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49 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
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50
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51 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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53 with open(myBigBedFilePath, 'w') as bigBedFile:
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54 subtools.bedToBigBed(sorted_biGenePred_file.name,
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55 self.chromSizesFile.name,
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56 bigBedFile.name,
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57 autoSql=auto_sql_option,
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58 typeOption='bed12+8',
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59 tab=True,
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60 extraIndex='name')
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62 # Create the Track Object
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63 self.createTrack(file_path=trackName,
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64 track_name=trackName,
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65 long_label=self.long_label,
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66 track_type='bigGenePred', visibility='dense',
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67 priority=self.priority,
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68 track_file=myBigBedFilePath,
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69 track_color=self.track_color,
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70 group_name=self.group_name,
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71 database=self.database)
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72
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73 print("- Gff3 %s created" % self.name_gff3)