Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/index/TrixIndex.py @ 50:804e7217f27c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty
author yating-l
date Fri, 20 Jul 2018 11:38:01 -0400
parents 31a41ce128cc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
25
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
1 #!/usr/bin/python
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
2
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
3 import os
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
4 import collections
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
5 import shutil
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
6 import logging
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
7 from ExternIndex import ExternIndex
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
8
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
9 class TrixIndex(ExternIndex):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
11 self.logger = logging.getLogger(__name__)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
12 self.indexIx = indexIx
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
13 self.indexIxx = indexIxx
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
14 self.trackName = trackName
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
15 self.mySpecieFolderPath = mySpecieFolderPath
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
16 self.trixId = trixId.strip()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
17 if not self.trixId:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
18 self.logger.error("Didn't specify the Trix identifier. To use TRIX index, you need to specify the identifier")
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
19 exit(1)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
20 if "default_index" in args:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
21 self.default_index = args["default_index"]
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
22 else:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
23 self.default_index = None
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
24 self.index_settings = collections.OrderedDict()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
25
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
26 def setExtLink(self):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
27 self.setSearchIndex()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
28 self.moveIndexFile()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
29 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
30 return self.index_settings
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
31
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
32 def moveIndexFile(self):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
33 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
34 self.indexIxName = "".join( ( self.trackName, ".ix") )
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
35 self.indexIxxName = "".join( ( self.trackName, ".ixx") )
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
36 if not os.path.exists(indexFolder):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
37 os.makedirs(indexFolder)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
38
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
39 # Move index files to the index folder
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
40 self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
41 shutil.copyfile(self.indexIx, self.indexIxPath)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
42 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
43 shutil.copyfile(self.indexIxx, self.indexIxxPath)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
44
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
45 def setSearchIndex(self):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
46 if self.default_index:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
47 set_index = set()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
48 set_index.add(self.trixId)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
49 set_index.add(self.default_index)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
50 search_index = ",".join(set_index)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
51 else:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
52 search_index = self.trixId
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
53 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
54 self.index_settings["searchIndex"] = search_index
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
55