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annotate Psl.py @ 23:2677f1899aa8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author yating-l
date Tue, 09 May 2017 15:42:43 -0400
parents c02720d1afee
children df42241d3731
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rmarenco
parents:
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1 import logging
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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2 import os
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rmarenco
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3 import tempfile
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rmarenco
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rmarenco
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5 # Internal dependencies
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rmarenco
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6 from Datatype import Datatype
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rmarenco
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7 from util import subtools
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rmarenco
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10 class Psl(Datatype):
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rmarenco
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11 def __init__(self, input_psl_path, data_psl):
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12 super(Psl, self).__init__()
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rmarenco
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14 self.track = None
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16 self.input_psl_path = input_psl_path
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rmarenco
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17 self.name_psl = data_psl["name"]
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18 self.priority = data_psl["order_index"]
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rmarenco
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19 self.track_color = data_psl["track_color"]
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rmarenco
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20 # TODO: Think about how to avoid repetition of the group_name everywhere
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rmarenco
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21 self.group_name = data_psl["group_name"]
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yating-l
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22 if data_psl["long_label"]:
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yating-l
parents: 17
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23 self.long_label = data_psl["long_label"]
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yating-l
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24 else:
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yating-l
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25 self.long_label = self.name_psl
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26 # Temporary files
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rmarenco
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27 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
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rmarenco
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28 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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rmarenco
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30 # Get the bed12+12 with pslToBigPsl
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rmarenco
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31 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
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rmarenco
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33 # Sort the formatted psl into sorted_bed_formatted_psl_file
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34 subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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36 # Get the binary indexed bigPsl with bedToBigBed
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37 trackName = "".join((self.name_psl, ".bb"))
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39 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
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41 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
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43 logging.debug("Hello")
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45 with open(my_big_psl_file_path, 'w') as big_psl_file:
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46 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
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47 self.chromSizesFile.name,
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48 big_psl_file.name,
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49 autoSql=auto_sql_option,
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50 typeOption='bed12+12',
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51 tab=True)
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53 # Create the Track Object
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54 self.createTrack(file_path=trackName,
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55 track_name=trackName,
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yating-l
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56 long_label=self.long_label,
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57 track_type='bigPsl', visibility='dense',
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58 priority=self.priority,
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59 track_file=my_big_psl_file_path,
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rmarenco
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60 track_color=self.track_color,
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61 group_name=self.group_name)
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63 print("- BigPsl %s created" % self.name_psl)