Mercurial > repos > rmarenco > hubarchivecreator
comparison BigWig.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
| author | rmarenco |
|---|---|
| date | Wed, 13 Jul 2016 13:36:37 -0400 |
| parents | |
| children | acc233161f50 |
comparison
equal
deleted
inserted
replaced
| 0:0f3bc17e5ede | 1:fb5e60d4d18a |
|---|---|
| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import shutil | |
| 5 | |
| 6 # Internal dependencies | |
| 7 from Datatype import Datatype | |
| 8 from Track import Track | |
| 9 from TrackDb import TrackDb | |
| 10 | |
| 11 | |
| 12 class BigWig( Datatype ): | |
| 13 def __init__(self, input_bigwig_path, data_bigwig, | |
| 14 input_fasta_path, extra_files_path, tool_directory): | |
| 15 super(BigWig, self).__init__( | |
| 16 input_fasta_path, extra_files_path, tool_directory | |
| 17 ) | |
| 18 | |
| 19 self.track = None | |
| 20 | |
| 21 self.input_bigwig_path = input_bigwig_path | |
| 22 self.name_bigwig = data_bigwig["name"] | |
| 23 self.priority = data_bigwig["order_index"] | |
| 24 | |
| 25 print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig ) | |
| 26 | |
| 27 trackName = "".join( ( self.name_bigwig, ".bigwig" ) ) | |
| 28 | |
| 29 myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 30 shutil.copy(self.input_bigwig_path, myBigWigFilePath) | |
| 31 | |
| 32 # Create the Track Object | |
| 33 dataURL = "tracks/%s" % trackName | |
| 34 | |
| 35 # Return the BigBed track | |
| 36 trackDb = TrackDb( | |
| 37 trackName=trackName, | |
| 38 longLabel=self.name_bigwig, | |
| 39 shortLabel=self.getShortName( self.name_bigwig ), | |
| 40 trackDataURL=dataURL, | |
| 41 trackType='bigWig', | |
| 42 visibility='full', | |
| 43 priority=self.priority, | |
| 44 ) | |
| 45 | |
| 46 self.track = Track( | |
| 47 trackFile=myBigWigFilePath, | |
| 48 trackDb=trackDb, | |
| 49 ) | |
| 50 | |
| 51 print("- %s created in %s" % (trackName, myBigWigFilePath)) |