Mercurial > repos > rmarenco > hubarchivecreator
view Bam.py @ 23:2677f1899aa8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author | yating-l |
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date | Tue, 09 May 2017 15:42:43 -0400 |
parents | 884ee2a71680 |
children | df42241d3731 |
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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 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"] if self.data_bam["long_label"]: self.long_label = self.data_bam["long_label"] else: self.long_label = self.name_bam # 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.long_label, 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))