Mercurial > repos > rmarenco > hubarchivecreator
view bigPsl.py @ 23:2677f1899aa8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author | yating-l |
---|---|
date | Tue, 09 May 2017 15:42:43 -0400 |
parents | 884ee2a71680 |
children | df42241d3731 |
line wrap: on
line source
#!/usr/bin/python import os import tempfile import string from Datatype import Datatype from Track import Track from TrackDb import TrackDb from util import subtools class bigPsl( Datatype ): def __init__(self, input_bigpsl_false_path, data_bigpsl): super(bigPsl, self).__init__() self.input_bigpsl_false_path = input_bigpsl_false_path self.name_bigpsl = data_bigpsl["name"] self.priority = data_bigpsl["order_index"] self.track_color = data_bigpsl["track_color"] # TODO: Think about how to avoid repetition of the group_name everywhere self.group_name = data_bigpsl["group_name"] if data_bigpsl["long_label"]: self.long_label = data_bigpsl["long_label"] else: self.long_label = self.name_bigpsl #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") # Sort processing #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) # bedToBigBed processing # TODO: Change the name of the bb, to tool + genome + .bb trackName = "".join( ( self.name_bigpsl, '.bb' ) ) myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') with open(myBigBedFilePath, 'w') as bigBedFile: subtools.bedToBigBed(self.input_bigpsl_false_path, self.chromSizesFile.name, bigBedFile.name, typeOption='bed12+12', tab='True', autoSql=auto_sql_option) self.createTrack(file_path=trackName, track_name=trackName, long_label=self.long_label, track_type='bigPsl', 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_simple_repeats, # shortLabel=self.getShortName( self.name_bed_simple_repeats ), # trackDataURL=dataURL, # trackType='bigBed 4 +', # visibility='dense', # priority=self.priority, # ) # # self.track = Track( # trackFile=myBigBedFilePath, # trackDb=trackDb, # ) print("- bigPsl %s created" % self.name_bigpsl) #print("- %s created in %s" % (trackName, myBigBedFilePath))