diff Datatype.py @ 1:fb5e60d4d18a draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Datatype.py	Wed Jul 13 13:36:37 2016 -0400
@@ -0,0 +1,36 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Super Class of the managed datatype
+"""
+
+import os
+
+from util import subtools
+
+
+class Datatype(object):
+    def __init__( self, input_fasta_file, extra_files_path, tool_directory ):
+
+        self.input_fasta_file = input_fasta_file
+        self.extra_files_path = extra_files_path
+        self.tool_directory = tool_directory
+
+
+        # Construction of the arborescence
+        # TODO: Change the hard-coded path with a input based one
+        self.mySpecieFolderPath = os.path.join(extra_files_path, "myHub", "dbia3")
+
+        # TODO: Refactor the name of the folder "tracks" into one variable, and should be inside TrackHub object
+        self.myTrackFolderPath = os.path.join(self.mySpecieFolderPath, "tracks")
+
+        # TODO: Redundant, should be refactored because they are all doing it...into hubArchiveCreator?
+        # 2bit file creation from input fasta
+        self.twoBitFile = subtools.faToTwoBit(self.input_fasta_file, self.mySpecieFolderPath)
+
+    def getShortName( self, name_to_shortify ):
+        # Slice to get from Long label the short label
+        short_label_slice = slice(0, 15)
+
+        return name_to_shortify[short_label_slice]
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