Mercurial > repos > rmarenco > hubarchivecreator

comparison BigBed.py @ 24:fcc1021bd496 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author yating-l
date Wed, 31 May 2017 11:35:16 -0400
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children df42241d3731
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23:2677f1899aa8 24:fcc1021bd496
1 #!/usr/bin/python
2
3 import os
4 import shutil
5 from subprocess import Popen, PIPE
6 import re
7
8 # Internal dependencies
9 from Datatype import Datatype
10
11 class BigBed(Datatype):
12 """ Configurations for creating the bigBed evidence track """
13
14 def __init__(self, input_bigbed_path, data_bigbed):
15 super(BigBed, self).__init__()
16
17 self.track = None
18
19 self.input_bigbed_path = input_bigbed_path
20 self.name_bigbed = data_bigbed["name"]
21 self.priority = data_bigbed["order_index"]
22 self.track_color = data_bigbed["track_color"]
23 self.group_name = data_bigbed["group_name"]
24
25 track_name = "".join((self.name_bigbed, ".bigbed"))
26 if data_bigbed["long_label"]:
27 self.long_label = data_bigbed["long_label"]
28 else:
29 self.long_label = self.name_bigbed
30
31 bigbed_file_path = os.path.join(self.myTrackFolderPath, track_name)
32
33 track_type = self.determine_track_type(input_bigbed_path)
34
35 shutil.copy(self.input_bigbed_path, bigbed_file_path)
36
37 # Create the Track Object
38 self.createTrack(file_path=track_name,
39 track_name=track_name,
40 long_label=self.long_label,
41 track_type=track_type,
42 visibility='hide',
43 priority=self.priority,
44 track_file=bigbed_file_path,
45 track_color=self.track_color,
46 group_name=self.group_name)
47
48 print "- BigBed %s created" % self.name_bigbed
49
50
51 def determine_track_type(self, bb_file):
52 """
53 Determine the number of standard and extra fields using bigBedSummary
54
55 Implementation of reading from stdout is based on a Stackoverflow post:
56 http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate
57
58 :param bb_file: path to a bigBed file
59
60 :returns: the bigBed track type
61 """
62
63 cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"],
64 stdout=PIPE, bufsize=1)
65
66 pattern = r"(\d+) bed definition fields, (\d+) total fields"
67
68 with cmd_ph.stdout:
69 for line in iter(cmd_ph.stdout.readline, b''):
70 match = re.match(pattern, line)
71
72 if match:
73 extra_mark = "." if match.group(1) == match.group(2) else "+"
74 bed_type = "bigBed %s %s" % (match.group(1), extra_mark)
75 break
76
77 cmd_ph.wait()
78
79 return bed_type