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annotate Psl.py @ 63:e50fc56bd10d draft

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author yating-l
date Wed, 09 Aug 2017 16:38:02 -0400
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1 import logging
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2 import os
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3 import tempfile
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5 # Internal dependencies
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6 from Datatype import Datatype
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7 from util import subtools
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10 class Psl(Datatype):
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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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14 self.track = None
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16 self.input_psl_path = input_psl_path
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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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19 self.track_color = data_psl["track_color"]
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20 # TODO: Think about how to avoid repetition of the group_name everywhere
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21 self.group_name = data_psl["group_name"]
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22 self.database = data_psl["database"]
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23 if data_psl["long_label"]:
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24 self.long_label = data_psl["long_label"]
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25 else:
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26 self.long_label = self.name_psl
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27 # Temporary files
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28 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
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29 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
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31 # Get the bed12+12 with pslToBigPsl
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32 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
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34 # Sort the formatted psl into sorted_bed_formatted_psl_file
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35 subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
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37 # Get the binary indexed bigPsl with bedToBigBed
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38 trackName = "".join((self.name_psl, ".bb"))
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40 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
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42 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
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44 logging.debug("Hello")
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46 with open(my_big_psl_file_path, 'w') as big_psl_file:
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47 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
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48 self.chromSizesFile.name,
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49 big_psl_file.name,
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50 autoSql=auto_sql_option,
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51 typeOption='bed12+12',
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52 tab=True,
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53 extraIndex='name')
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55 # Create the Track Object
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56 self.createTrack(file_path=trackName,
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57 track_name=trackName,
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58 long_label=self.long_label,
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59 track_type='bigPsl', visibility='dense',
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60 priority=self.priority,
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61 track_file=my_big_psl_file_path,
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62 track_color=self.track_color,
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63 group_name=self.group_name,
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64 database=self.database)
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66 print("- BigPsl %s created" % self.name_psl)