diff jbrowse_hub.py @ 5:e7c80e9b70ae draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

--- a/jbrowse_hub.py	Fri Mar 10 14:57:36 2017 -0500
+++ b/jbrowse_hub.py	Tue Mar 14 12:24:37 2017 -0400
@@ -10,6 +10,7 @@
 import tempfile
 import trackObject
 import TrackHub
+import shutil
 
 def main(argv):
     parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
@@ -17,8 +18,14 @@
     # Reference genome mandatory
     parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
 
+    # Genome name
+    parser.add_argument('-g', '--genome_name', help='Name of reference genome')
+
     # Output folder
-    parser.add_argument('-o', '--out', help='Name of the HTML summarizing the content of the JBrowse Hub')
+    parser.add_argument('-o', '--out', help='output html')
+
+    # Output folder
+    parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")
 
     # GFF3
     parser.add_argument('--gff3', action='append', help='GFF3 format')
@@ -45,12 +52,23 @@
 
     args = parser.parse_args()
     all_datatype_dictionary = dict()
-    all_tracks = []
+    
 
     reference = args.fasta
-    out_path = args.out
-    tool_directory = 'JBrowse-1.12.1/bin'
-    chrom_size = utils.getChromSizes(reference, '../ucsc_tools_340_for_HAC')
+    genome = 'unknown'
+    out_path = '.'
+    extra_files_path = '.'
+    if args.genome_name:
+        genome = utils.sanitize_name_path(args.genome_name)
+    if args.out:
+        out_path = args.out
+    if args.extra_files_path:
+        extra_files_path = utils.sanitize_name_path(args.extra_files_path)
+    cwd = os.getcwd()
+    #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
+    tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin')
+    chrom_size = utils.getChromSizes(reference, tool_directory)
+    all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
     array_inputs_bam = args.bam
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
@@ -77,21 +95,19 @@
 
     for datatype, inputfiles in all_datatype_dictionary.items():
         try:
-            user_input = inputfiles
-            if not user_input:
+            if not inputfiles:
                 raise ValueError('empty input, must provide track files!\n')
         except IOError:
             print 'Cannot open', datatype
         else:
             for f in inputfiles:
-                track = trackObject.trackObject(f, datatype, chrom_size.name)
-                track.addToRaw()
-                all_tracks.append(track)
+                all_tracks.addToRaw(f, datatype)
 
-    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory)
+    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path)
     jbrowseHub.createHub()
-            
-            
+         
+    
+
 '''
     if reference:
         p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])