changeset 68:f9d7a9f9d796 draft

Deleted selected files

--- a/Reader.py	Tue Sep 26 17:55:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-import json
-import logging
-import codecs
-
-
-# Internal dependencies
-from datatypes.binary.Bam import Bam
-from datatypes.binary.BigWig import BigWig
-from datatypes.binary.BigBed import BigBed
-from datatypes.interval.Bed import Bed
-from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats
-from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions
-from datatypes.interval.CytoBand import CytoBand
-from datatypes.interval.BedBlatAlignments import BedBlatAlignments
-from datatypes.interval.BedBlastAlignments import BedBlastAlignments
-from datatypes.interval.Gff3 import Gff3
-from datatypes.interval.Gtf import Gtf
-from datatypes.interval.Psl import Psl
-from datatypes.sequence.Fasta import Fasta
-from util import santitizer
-
-class Reader(object):
-    
-    DATATYPE_CLASS = [Bam, BigWig, BigBed, Bed, BedSimpleRepeats, BedSpliceJunctions, CytoBand, BedBlatAlignments, BedBlastAlignments, Gff3, Gtf, Psl, Fasta]
-
-    def __init__(self, input_json_file):
-        self.inputFile = input_json_file
-        self.args = self.loadJson()
-        
-    
-    def loadJson(self):
-        try:
-            data_file = codecs.open(self.inputFile, 'r', 'utf-8')   
-            return json.load(data_file) 
-        except IOError:
-            print "Cannot find JSON file\n"
-            exit(1)
-
-    def getToolDir(self):
-        try:
-            return self.args["tool_directory"]
-        except KeyError:
-            print ("tool_directory is not defined in the input file!")
-            exit(1)
-
-    def getExtFilesPath(self):
-        try:
-            return self.args["extra_files_path"]
-        except KeyError:
-            print ("extra_files_path is not defined in the input file!")
-            exit(1)
-
-    def getUserEmail(self):
-        try:
-            return self.args["user_email"]
-        except KeyError:
-            print ("user_email is not defined in the input file!")
-            exit(1)
-    
-    def getDebugMode(self):
-        try:
-            return self.args["debug_mode"]
-        except KeyError:
-            print ("debug_mode is not defined in the input file!")
-            exit(1)
-        
-        
-    def getRefGenome(self):
-        array_inputs_reference_genome = self.args["fasta"]
-        # TODO: Replace these with the object Fasta
-        input_fasta_file = array_inputs_reference_genome["false_path"]
-        input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
-        genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
-        reference_genome = Fasta(input_fasta_file,
-                             input_fasta_file_name, genome_name)
-        return reference_genome
-    
-
-    def getTracksData(self):
-        self.logger = logging.getLogger(__name__)
-        all_datatype_dictionary = dict()
-        for datatype in self.DATATYPE_CLASS:
-            class_name = datatype.__name__
-            array_inputs = self.args.get(str(class_name))
-            if array_inputs:
-                self.logger.debug("Create %s objects\n", class_name)
-                self.logger.debug("array_inputs: %s", array_inputs)
-                all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
-               
-        return all_datatype_dictionary
-
-    def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
-        """
-        Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
-        and update the dictionary of datatype
-
-        :param ExtensionClass:
-        :param array_inputs:
-        :type ExtensionClass: Datatype
-        :type array_inputs: list[string]
-        """
-
-        datatype_dictionary = {}
-
-        # TODO: Optimize this double loop
-        for input_data in array_inputs:
-            input_false_path = input_data["false_path"]
-            santitizer.sanitize_name_input(input_data["name"])
-            extensionObject = ExtensionClass(input_false_path, input_data)
-            extensionObject.generateCustomTrack()
-            datatype_dictionary.update({input_data["order_index"]: extensionObject})
-        return datatype_dictionary
-
-    
-        
-
-