Mercurial > repos > rmarenco > hubarchivecreator

annotate Psl.py @ 18:d786bca6a75d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3007f4ce1d6e8ac8324970d355f028b9394e2a5f
author rmarenco
date Fri, 30 Sep 2016 18:33:03 -0400
parents c02720d1afee
children 2677f1899aa8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
1 import logging
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
2 import os
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
3 import tempfile
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
4
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
5 # Internal dependencies
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
6 from Datatype import Datatype
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
7 from util import subtools
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
8
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
9
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
10 class Psl(Datatype):
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
11 def __init__(self, input_psl_path, data_psl):
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
12 super(Psl, self).__init__()
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
13
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
14 self.track = None
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
15
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
16 self.input_psl_path = input_psl_path
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
17 self.name_psl = data_psl["name"]
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
18 self.priority = data_psl["order_index"]
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
19 self.track_color = data_psl["track_color"]
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
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
parents: 16
diff changeset
21 self.group_name = data_psl["group_name"]
16
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
22
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
23 # Temporary files
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
24 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
25 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
26
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
27 # Get the bed12+12 with pslToBigPsl
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
29
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
32
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
33 # Get the binary indexed bigPsl with bedToBigBed
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
34 trackName = "".join((self.name_psl, ".bb"))
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
35
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
37
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
39
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
40 logging.debug("Hello")
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
41
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
43 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
44 self.chromSizesFile.name,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
45 big_psl_file.name,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
46 autoSql=auto_sql_option,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
47 typeOption='bed12+12',
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
48 tab=True)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
49
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
50 # Create the Track Object
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
51 self.createTrack(file_path=trackName,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
52 track_name=trackName,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
53 long_label=self.name_psl,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
54 track_type='bigPsl', visibility='dense',
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
55 priority=self.priority,
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
56 track_file=my_big_psl_file_path,
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
57 track_color=self.track_color,
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
58 group_name=self.group_name)
16
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
59
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff changeset
60 print("- BigPsl %s created" % self.name_psl)