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annotate Psl.py @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children 2677f1899aa8
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3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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3 import tempfile
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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5 # Internal dependencies
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rmarenco
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6 from Datatype import Datatype
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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7 from util import subtools
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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10 class Psl(Datatype):
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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11 def __init__(self, input_psl_path, data_psl):
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12 super(Psl, self).__init__()
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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14 self.track = None
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16 self.input_psl_path = input_psl_path
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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17 self.name_psl = data_psl["name"]
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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18 self.priority = data_psl["order_index"]
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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19 self.track_color = data_psl["track_color"]
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c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
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20 # TODO: Think about how to avoid repetition of the group_name everywhere
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
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21 self.group_name = data_psl["group_name"]
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23 # Temporary files
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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24 unsorted_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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25 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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27 # Get the bed12+12 with pslToBigPsl
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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28 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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30 # Sort the formatted psl into sorted_bed_formatted_psl_file
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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31 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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3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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33 # Get the binary indexed bigPsl with bedToBigBed
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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34 trackName = "".join((self.name_psl, ".bb"))
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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36 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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38 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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40 logging.debug("Hello")
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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42 with open(my_big_psl_file_path, 'w') as big_psl_file:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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43 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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44 self.chromSizesFile.name,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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45 big_psl_file.name,
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rmarenco
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46 autoSql=auto_sql_option,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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47 typeOption='bed12+12',
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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48 tab=True)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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50 # Create the Track Object
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51 self.createTrack(file_path=trackName,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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52 track_name=trackName,
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53 long_label=self.name_psl,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
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54 track_type='bigPsl', visibility='dense',
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rmarenco
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55 priority=self.priority,
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56 track_file=my_big_psl_file_path,
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57 track_color=self.track_color,
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rmarenco
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58 group_name=self.group_name)
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60 print("- BigPsl %s created" % self.name_psl)