Mercurial > repos > rmarenco > hubarchivecreator
view Bam.py @ 17:c02720d1afee draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author | rmarenco |
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date | Fri, 30 Sep 2016 15:14:24 -0400 |
parents | 3233451a3bd6 |
children | 884ee2a71680 |
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#!/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))