--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse_hub.py	Wed Apr 12 17:41:55 2017 -0400
@@ -0,0 +1,171 @@
+#!/usr/bin/env python
+
+import sys
+import argparse
+import json
+import utils
+import trackObject
+import TrackHub
+
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
+
+    # Reference genome mandatory
+    parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome (Required)')
+
+    # Genome name
+    parser.add_argument('-g', '--genome_name', help='Name of reference genome')
+
+    # Output folder
+    parser.add_argument('-o', '--out', help='output html')
+
+    # Output folder
+    parser.add_argument('-e', '--extra_files_path', help='Directory of JBrowse Hub folder')
+
+    #Tool Directory
+    parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools')
+
+    #GFF3
+    parser.add_argument('--gff3', action='append', help='GFF3 format')
+
+    # GFF3 structure: gene->transcription->CDS
+    parser.add_argument('--gff3_transcript', action='append', help='GFF3 format for gene prediction, structure: gene->transcription->CDS')
+
+    # GFF3 structure: gene->mRNA->CDS
+    parser.add_argument('--gff3_mrna', action='append', help='GFF3 format for gene prediction, structure: gene->mRNA->CDS')
+
+    # generic BED 
+    parser.add_argument('--bed', action='append', help='BED format')
+
+    # trfBig simple repeats (BED 4+12)
+    parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
+
+    # regtools (BED 12+1)
+    parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
+
+    # tblastn alignment (blastxml)
+    parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
+
+    # BAM format
+    parser.add_argument('--bam', action='append', help='BAM format from HISAT')
+
+    # BIGWIG format
+    parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
+
+    # GTF format
+    parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
+
+    # Metadata json format
+    parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
+
+    #JBrowse host
+    parser.add_argument('--jbrowse_host', help="JBrowse Host")
+
+    args = parser.parse_args()
+    all_datatype_dictionary = dict()
+    
+
+    if not args.fasta:
+        parser.print_help()
+        raise RuntimeError("No reference genome\n")
+    reference = args.fasta
+    genome = 'unknown'
+    out_path = 'unknown.html'
+    extra_files_path = '.'
+    tool_directory = '.'
+    jbrowse_host = ''
+    if args.jbrowse_host:
+        jbrowse_host = args.jbrowse_host
+    if args.genome_name:
+        genome = args.genome_name
+    if args.out:
+        out_path = args.out
+    if args.extra_files_path:
+        extra_files_path = args.extra_files_path
+
+    #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
+    if args.tool_directory:
+        tool_directory = args.tool_directory
+
+    #Calculate chromsome sizes using genome reference and uscs tools
+    chrom_size = utils.getChromSizes(reference, tool_directory)
+
+    #get metadata from json file
+    json_inputs_data = args.data_json
+    if json_inputs_data:
+        inputs_data = json.loads(json_inputs_data)
+    else:
+        inputs_data = {}
+    
+    #print inputs_data
+
+    #Initate trackObject
+    all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) 
+    
+    array_inputs_bam = args.bam
+    array_inputs_bed = args.bed
+    array_inputs_bed_simple_repeats = args.bedSimpleRepeats
+    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
+    array_inputs_bigwig = args.bigwig
+    array_inputs_gff3 = args.gff3
+    array_inputs_gff3_transcript = args.gff3_transcript
+    array_inputs_gff3_mrna = args.gff3_mrna
+    array_inputs_gtf = args.gtf
+    array_inputs_blastxml = args.blastxml
+
+    if array_inputs_bam:
+        all_datatype_dictionary['bam'] = array_inputs_bam
+    if array_inputs_bed:
+        all_datatype_dictionary['bed'] = array_inputs_bed
+    if array_inputs_bed_simple_repeats:
+        all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
+    if array_inputs_bed_splice_junctions:
+        all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
+    if array_inputs_bigwig:
+        all_datatype_dictionary['bigwig'] = array_inputs_bigwig
+    if array_inputs_gff3:
+        all_datatype_dictionary['gff3'] = array_inputs_gff3
+    if array_inputs_gff3_transcript:
+        all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
+    if array_inputs_gff3_mrna:
+        all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
+    if array_inputs_gtf:
+        all_datatype_dictionary['gtf'] = array_inputs_gtf
+    if array_inputs_blastxml:
+        all_datatype_dictionary['blastxml'] = array_inputs_blastxml
+    
+    print "input tracks: \n", all_datatype_dictionary
+
+    for datatype, inputfiles in all_datatype_dictionary.items():
+        try:
+            if not inputfiles:
+                raise ValueError('empty input, must provide track files!\n')
+        except IOError:
+            print 'Cannot open', datatype
+        else:
+            for f in inputfiles:
+                #metadata = {}
+                #print f
+                #if f in inputs_data.keys():
+                   # metadata = inputs_data[f]
+                    #print metadata
+                #Convert tracks into gff3 format
+                all_tracks.addToRaw(f, datatype)
+
+    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data, jbrowse_host)
+    jbrowseHub.createHub()
+
+"""        
+def extractMetadata(array_inputs, inputs_data):
+    metadata_dict = {}
+    for input_false_path in array_inputs:
+        for key, data_value in inputs_data.items():
+            if key == input_false_path:
+                metadata_dict[input_false_path]
+"""
+
+if __name__ == "__main__":
+    main(sys.argv)
+