Mercurial > repos > rmarenco > hubarchivecreator

comparison Psl.py @ 16:3233451a3bd6 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
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children c02720d1afee
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15:2a45cd656e8e 16:3233451a3bd6
1 import logging
2 import os
3 import tempfile
4
5 # Internal dependencies
6 from Datatype import Datatype
7 from util import subtools
8
9
10 class Psl(Datatype):
11 def __init__(self, input_psl_path, data_psl):
12 super(Psl, self).__init__()
13
14 self.track = None
15
16 self.input_psl_path = input_psl_path
17 self.name_psl = data_psl["name"]
18 self.priority = data_psl["order_index"]
19 self.track_color = data_psl["track_color"]
20
21 # Temporary files
22 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
23 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
24
25 # Get the bed12+12 with pslToBigPsl
26 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
27
28 # Sort the formatted psl into sorted_bed_formatted_psl_file
29 subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
30
31 # Get the binary indexed bigPsl with bedToBigBed
32 trackName = "".join((self.name_psl, ".bb"))
33
34 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
35
36 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
37
38 logging.debug("Hello")
39
40 with open(my_big_psl_file_path, 'w') as big_psl_file:
41 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
42 self.chromSizesFile.name,
43 big_psl_file.name,
44 autoSql=auto_sql_option,
45 typeOption='bed12+12',
46 tab=True)
47
48 # Create the Track Object
49 self.createTrack(file_path=trackName,
50 track_name=trackName,
51 long_label=self.name_psl,
52 track_type='bigPsl', visibility='dense',
53 priority=self.priority,
54 track_file=my_big_psl_file_path,
55 track_color=self.track_color)
56
57 print("- BigPsl %s created" % self.name_psl)