comparison TrackHub.py @ 66:4ca7cbf2d9b8 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty

65:5a4206366b41

import logging
import os
import tempfile
import shutil
import zipfile

# Internal dependencies
from Datatype import Datatype
from util import subtools

from mako.lookup import TemplateLookup


class TrackHub(object):
    """docstring for TrackHub"""

    def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
        super(TrackHub, self).__init__()

        self.rootAssemblyHub = None

        self.mySpecieFolderPath = None
        self.myTracksFolderPath = None
        self.tool_directory = tool_directory

        # Init the Datatype
        Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
                          self.extra_files_path, self.tool_directory,
                          self.mySpecieFolderPath, self.myTracksFolderPath)

    def createZip(self):
        for root, dirs, files in os.walk(self.rootAssemblyHub):
            # Get all files and construct the dir at the same time
            for file in files:
                self.outputZip.write(os.path.join(root, file))

        self.outputZip.close()

    def addTrack(self, trackDbObject=None):
        # Create the trackDb.txt file in the specie folder, if not exists
        # Else append the new track
        # TODO: Get this out of the function
        trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')

        # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
        with open(trackDbTxtFilePath, 'a+') as trackDbFile:
            trackDbs = [trackDbObject]

            # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
            # Add the group as well, if exists in trackDbObject
            self.addGroup(trackDbObject.group_name)

            htmlMakoRendered = self.trackDbTemplate.render(
                trackDbs=trackDbs
            )
            trackDbFile.write(htmlMakoRendered)

        logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName,
                                                                  trackDbObject.group_name.lower().replace(' ', '_')))

    def addGroup(self, group_name="Default"):
        # If not already present in self.groups, add to groups.txt
        # Create the trackDb.txt file in the specie folder, if not exists
        # Else append the new track
        # TODO: Get this out of the function

            htmlMakoRendered = mytemplate.render(
                walkable_tree=walkable_tree
            )
            htmlOutput.write(htmlMakoRendered)

    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta

        # baseNameFasta = os.path.basename(fasta_file_name)

66:4ca7cbf2d9b8

import logging
import os
import tempfile
import shutil
import zipfile
from mako.lookup import TemplateLookup

# Internal dependencies
from datatypes.Datatype import Datatype
from util import subtools




class TrackHub(object):
    """docstring for TrackHub"""

    def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
        super(TrackHub, self).__init__()
        self.rootAssemblyHub = None

        self.mySpecieFolderPath = None
        self.myTracksFolderPath = None
        self.tool_directory = tool_directory

        # Init the Datatype
        Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
                          self.extra_files_path, self.tool_directory,
                          self.mySpecieFolderPath, self.myTracksFolderPath)
    '''
    def createZip(self):
        for root, dirs, files in os.walk(self.rootAssemblyHub):
            # Get all files and construct the dir at the same time
            for file in files:
                self.outputZip.write(os.path.join(root, file))

        self.outputZip.close()
    '''
    def addTrack(self, trackDbObject=None):
        # Create the trackDb.txt file in the specie folder, if not exists
        # Else append the new track
        # TODO: Get this out of the function
        trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
        # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
        with open(trackDbTxtFilePath, 'a+') as trackDbFile:
            trackDbs = [trackDbObject]

            # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
            # Add the group as well, if exists in trackDbObject
            self.addGroup(trackDbObject["group"])

            htmlMakoRendered = self.trackDbTemplate.render(
                trackDbs=trackDbs
            )
            trackDbFile.write(htmlMakoRendered)

        #logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName,
        #                                                          trackDbObject.group_name.lower().replace(' ', '_')))
        logging.debug("We just added track {0} (in group {1})".format(trackDbObject.get("track"),
                                                                  trackDbObject.get("group").lower().replace(' ', '_')))
    def addGroup(self, group_name="Default"):
        # If not already present in self.groups, add to groups.txt
        # Create the trackDb.txt file in the specie folder, if not exists
        # Else append the new track
        # TODO: Get this out of the function

            htmlMakoRendered = mytemplate.render(
                walkable_tree=walkable_tree
            )
            htmlOutput.write(htmlMakoRendered)


    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta

        # baseNameFasta = os.path.basename(fasta_file_name)