annotate hub-archive-creator/Psl.py @ 6:9193fe3ee73f draft default tip

Uploaded
author yating-l
date Thu, 22 Dec 2016 15:59:24 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
1 import logging
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
2 import os
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
3 import tempfile
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
4
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
5 # Internal dependencies
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
6 from Datatype import Datatype
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
7 from util import subtools
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
8
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
9
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
10 class Psl(Datatype):
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
11 def __init__(self, input_psl_path, data_psl):
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
12 super(Psl, self).__init__()
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
13
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
14 self.track = None
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
15
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
16 self.input_psl_path = input_psl_path
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
17 self.name_psl = data_psl["name"]
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
18 self.priority = data_psl["order_index"]
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
19 self.track_color = data_psl["track_color"]
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
20 # TODO: Think about how to avoid repetition of the group_name everywhere
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
21 self.group_name = data_psl["group_name"]
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
22
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
23 # Temporary files
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
24 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
25 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
26
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
27 # Get the bed12+12 with pslToBigPsl
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
28 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
29
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
30 # Sort the formatted psl into sorted_bed_formatted_psl_file
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
31 subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
32
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
33 # Get the binary indexed bigPsl with bedToBigBed
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
34 trackName = "".join((self.name_psl, ".bb"))
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
35
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
36 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
37
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
38 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
39
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
40 logging.debug("Hello")
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
41
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
42 with open(my_big_psl_file_path, 'w') as big_psl_file:
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
43 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
44 self.chromSizesFile.name,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
45 big_psl_file.name,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
46 autoSql=auto_sql_option,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
47 typeOption='bed12+12',
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
48 tab=True)
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
49
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
50 # Create the Track Object
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
51 self.createTrack(file_path=trackName,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
52 track_name=trackName,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
53 long_label=self.name_psl,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
54 track_type='bigPsl', visibility='dense',
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
55 priority=self.priority,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
56 track_file=my_big_psl_file_path,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
57 track_color=self.track_color,
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
58 group_name=self.group_name)
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
59
9193fe3ee73f Uploaded
yating-l
parents:
diff changeset
60 print("- BigPsl %s created" % self.name_psl)