# HG changeset patch # User yating-l # Date 1482440335 18000 # Node ID 48d7b2dddae6499a5978eb5231b5f35204927c6d # Parent 67fab89033f2d48286793dfd851b4f2188e1fb3a Deleted selected files diff -r 67fab89033f2 -r 48d7b2dddae6 Bam.py --- a/Bam.py Thu Dec 22 15:56:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -#!/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)) diff -r 67fab89033f2 -r 48d7b2dddae6 Bed.py --- a/Bed.py Thu Dec 22 15:56:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -# Internal dependencies -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class Bed( Datatype ): - def __init__( self, inputBedGeneric, data_bed_generic): - super(Bed, self).__init__() - - self.track = None - - self.inputBedGeneric = inputBedGeneric - - self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - self.data_bed_generic = data_bed_generic - self.name_bed_generic = self.data_bed_generic["name"] - self.priority = self.data_bed_generic["order_index"] - self.track_color = self.data_bed_generic["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = self.data_bed_generic["group_name"] - - - # Sort processing - subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb - trackName = "".join( ( self.name_bed_generic, ".bb") ) - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - with open(myBigBedFilePath, 'w') as self.bigBedFile: - subtools.bedToBigBed(self.sortedBedFile.name, - self.chromSizesFile.name, - self.bigBedFile.name) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name) - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_generic, - # shortLabel=self.getShortName(self.name_bed_generic), - # trackDataURL=dataURL, - # trackType='bigBed', - # visibility='dense', - # thickDrawItem='on', - # priority=self.priority, - # ) - # - # # Return the BigBed track - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed %s created" % self.name_bed_generic) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) diff -r 67fab89033f2 -r 48d7b2dddae6 hubarchivecreator --- a/hubarchivecreator Thu Dec 22 15:56:35 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,187 +0,0 @@ - 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Thu, 22 Dec 2016 15:32:27 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty - default tip -
Thu, 22 Dec 2016 14:21:03 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e61ffe1cf3150efe264a35e6287dc60a70d4e526 - -
Wed, 21 Dec 2016 18:00:09 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 48b59e91e2dcc2e97735ee35d587960cbfbce932 - -
Wed, 21 Dec 2016 17:26:51 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty - -
Wed, 21 Dec 2016 12:09:58 -0500yating-l - planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty - -
Wed, 21 Dec 2016 11:18:27 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty - -
Tue, 22 Nov 2016 17:13:18 -0500yating-l - planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty - -
Tue, 22 Nov 2016 17:07:47 -0500yating-l - Uploaded - -
Mon, 31 Oct 2016 16:36:25 -0400yating-l - planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty - -
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