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annotate Gff3.py @ 0:abcfd662b679 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
author yating-l
date Thu, 22 Dec 2016 17:53:00 -0500
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abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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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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26 # TODO: See if we need these temporary files as part of the generated files
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27 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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28 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
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29 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
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31 # gff3ToGenePred processing
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32 subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
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34 # genePredToBigGenePred
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35 subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
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37 # Sort processing
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38 subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
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40 # TODO: Check if no errors
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42 # bedToBigBed processing
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43 trackName = "".join( (self.name_gff3, ".bb" ) )
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45 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
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47 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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49 with open(myBigBedFilePath, 'w') as bigBedFile:
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50 subtools.bedToBigBed(sorted_biGenePred_file.name,
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51 self.chromSizesFile.name,
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52 bigBedFile.name,
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53 autoSql=auto_sql_option,
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54 typeOption='bed12+8',
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55 tab=True)
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56
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57 # Create the Track Object
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58 self.createTrack(file_path=trackName,
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59 track_name=trackName,
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60 long_label=self.name_gff3,
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61 track_type='bigGenePred', visibility='dense',
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62 priority=self.priority,
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63 track_file=myBigBedFilePath,
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64 track_color=self.track_color,
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65 group_name=self.group_name)
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66
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67 print("- Gff3 %s created" % self.name_gff3)