annotate Bam.py @ 22:7ddf651457df draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty

#!/usr/bin/python
# -*- coding: utf8 -*-

"""
Class to handle Bam files to UCSC TrackHub
"""

import logging
import os
import shutil

from Datatype import Datatype
from Track import Track
from TrackDb import TrackDb



class Bam( Datatype ):
    def __init__(self, input_bam_false_path, data_bam):
        super(Bam, self).__init__()

        self.track = None

        self.input_bam_false_path = input_bam_false_path

        self.data_bam = data_bam
        # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
        if ".bam" not in self.data_bam["name"]:
            self.name_bam = self.data_bam["name"] + ".bam"
        else:
            self.name_bam = self.data_bam["name"]

        self.priority = self.data_bam["order_index"]
        self.index_bam = self.data_bam["index"]
        # TODO: Think about how to avoid repetition of the color treatment
        self.track_color = self.data_bam["track_color"]

        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = self.data_bam["group_name"]

        # First: Add the bam file
        # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)

        bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
        shutil.copyfile(self.input_bam_false_path, bam_file_path)

        # Create and add the bam index file to the same folder
        name_index_bam = self.name_bam + ".bai"
        bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
        shutil.copyfile(self.index_bam, bam_index_file_path)

        # Create the Track Object
        self.createTrack(file_path=self.name_bam,
                         track_name=self.name_bam,
                         long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
                         track_file=bam_index_file_path,
                         track_color=self.track_color,
                         group_name=self.group_name
                         )
        #
        # dataURL = "tracks/%s" % self.name_bam
        #
        # trackDb = TrackDb(
        #     trackName=self.name_bam,
        #     longLabel=self.name_bam,
        #     shortLabel=self.getShortName( self.name_bam ),
        #     trackDataURL=dataURL,
        #     trackType='bam',
        #     visibility='pack',
        #     priority=self.priority,
        # )
        #
        # # Return the Bam Track Object
        # self.track = Track(
        #     trackFile=bam_index_file_path,
        #     trackDb=trackDb,
        # )

        print("- Bam %s created" % self.name_bam)
        #print("- %s created in %s" % (self.name_bam, bam_file_path))
        #print("- %s created in %s" % (self.index_bam, bam_index_file_path))