view Bam.py @ 27:6872b9583e26 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-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
from util import subtools


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))