diff util/Reader.py @ 39:4a69515eed63 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 91271a6c0d39c923f0d460b2979247baa297286b-dirty

--- a/util/Reader.py	Fri Apr 06 13:44:56 2018 -0400
+++ b/util/Reader.py	Fri Apr 13 18:21:35 2018 -0400
@@ -1,4 +1,6 @@
+import os
 import json
+import shutil
 import logging
 import codecs
 
@@ -67,8 +69,11 @@
             exit(1)
 
     def getTrackType(self):
-        track_type = self.args.get("track_type")
-        return track_type
+        try:
+            return self.args.get("feature_tracks_type")
+        except KeyError:
+            print ("feature tracks type is not defined in the input file!")
+            exit(1)
     
     def getGenomeName(self):
         genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
@@ -76,12 +81,13 @@
         
     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"])
+        # Add "fasta" extension because Apollo needs it to create annotation
+        refseq_file = os.path.join(os.path.dirname(input_fasta_file), input_fasta_file_name + ".fasta")
+        shutil.copyfile(input_fasta_file, refseq_file)
         genome_name = self.getGenomeName()
-        reference_genome = Fasta(input_fasta_file,
+        reference_genome = Fasta(refseq_file,
                              input_fasta_file_name, genome_name)
         return reference_genome