Mercurial > repos > yating-l > jbrowsearchivecreator
view util/index/TrixIndex.py @ 17:315a40b0b694 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc
author | yating-l |
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date | Mon, 25 Jun 2018 16:05:01 -0400 |
parents | 237707a6b74d |
children |
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#!/usr/bin/python import os import collections import shutil import logging from ExternIndex import ExternIndex class TrixIndex(ExternIndex): def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args): self.logger = logging.getLogger(__name__) self.indexIx = indexIx self.indexIxx = indexIxx self.trackName = trackName self.mySpecieFolderPath = mySpecieFolderPath self.trixId = trixId.strip() if not self.trixId: self.logger.error("Didn't specify the Trix identifier. To use TRIX index, you need to specify the identifier") exit(1) if "default_index" in args: self.default_index = args["default_index"] else: self.default_index = None self.index_settings = collections.OrderedDict() def setExtLink(self): self.setSearchIndex() self.moveIndexFile() self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName return self.index_settings def moveIndexFile(self): indexFolder = os.path.join(self.mySpecieFolderPath, 'trix') self.indexIxName = "".join( ( self.trackName, ".ix") ) self.indexIxxName = "".join( ( self.trackName, ".ixx") ) if not os.path.exists(indexFolder): os.makedirs(indexFolder) # Move index files to the index folder self.indexIxPath = os.path.join(indexFolder, self.indexIxName) shutil.copyfile(self.indexIx, self.indexIxPath) self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName) shutil.copyfile(self.indexIxx, self.indexIxxPath) def setSearchIndex(self): if self.default_index: set_index = set() set_index.add(self.trixId) set_index.add(self.default_index) search_index = ",".join(set_index) else: search_index = self.trixId logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index) self.index_settings["searchIndex"] = search_index