Mercurial > repos > yating-l > hubarchivecreator
comparison Gff3.py @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
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| date | Wed, 21 Dec 2016 12:13:04 -0500 |
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| children |
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| -1:000000000000 | 0:f493979f1408 |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import tempfile | |
| 5 | |
| 6 # Internal dependencies | |
| 7 from Datatype import Datatype | |
| 8 from Track import Track | |
| 9 from TrackDb import TrackDb | |
| 10 from util import subtools | |
| 11 | |
| 12 | |
| 13 class Gff3( Datatype ): | |
| 14 def __init__(self, input_Gff3_false_path, data_gff3): | |
| 15 super( Gff3, self ).__init__() | |
| 16 | |
| 17 self.track = None | |
| 18 | |
| 19 self.input_Gff3_false_path = input_Gff3_false_path | |
| 20 self.name_gff3 = data_gff3["name"] | |
| 21 self.priority = data_gff3["order_index"] | |
| 22 self.track_color = data_gff3["track_color"] | |
| 23 # TODO: Think about how to avoid repetition of the group_name everywhere | |
| 24 self.group_name = data_gff3["group_name"] | |
| 25 | |
| 26 # TODO: See if we need these temporary files as part of the generated files | |
| 27 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") | |
| 28 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") | |
| 29 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") | |
| 30 | |
| 31 # gff3ToGenePred processing | |
| 32 subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name) | |
| 33 | |
| 34 # genePredToBigGenePred | |
| 35 subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name) | |
| 36 | |
| 37 # Sort processing | |
| 38 subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name) | |
| 39 | |
| 40 # TODO: Check if no errors | |
| 41 | |
| 42 # bedToBigBed processing | |
| 43 trackName = "".join( (self.name_gff3, ".bb" ) ) | |
| 44 | |
| 45 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as') | |
| 46 | |
| 47 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 48 | |
| 49 with open(myBigBedFilePath, 'w') as bigBedFile: | |
| 50 subtools.bedToBigBed(sorted_biGenePred_file.name, | |
| 51 self.chromSizesFile.name, | |
| 52 bigBedFile.name, | |
| 53 autoSql=auto_sql_option, | |
| 54 typeOption='bed12+8', | |
| 55 tab=True) | |
| 56 | |
| 57 # Create the Track Object | |
| 58 self.createTrack(file_path=trackName, | |
| 59 track_name=trackName, | |
| 60 long_label=self.name_gff3, | |
| 61 track_type='bigGenePred', visibility='dense', | |
| 62 priority=self.priority, | |
| 63 track_file=myBigBedFilePath, | |
| 64 track_color=self.track_color, | |
| 65 group_name=self.group_name) | |
| 66 | |
| 67 print("- Gff3 %s created" % self.name_gff3) |