diff jbrowse_hub.py @ 0:e4f3f2ed4fa5 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse_hub.py	Fri Mar 10 13:48:19 2017 -0500
@@ -0,0 +1,181 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import argparse
+import subprocess
+from bedToGff3 import bedToGff3
+import blastxmlToGff3
+import utils
+import tempfile
+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')
+
+    # Output folder
+    parser.add_argument('-o', '--out', help='Name of the HTML summarizing the content of the JBrowse Hub')
+
+    # GFF3
+    parser.add_argument('--gff3', action='append', help='GFF3 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')
+    # put bam index file at the same directory with bam file
+    # parser.add_argument('--bai', action='append', help='BAM index 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')
+
+    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')
+    array_inputs_bam = args.bam
+    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_gtf = args.gtf
+    array_inputs_blastxml = args.blastxml
+    if array_inputs_bam:
+        all_datatype_dictionary['bam'] = array_inputs_bam
+    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_gtf:
+        all_datatype_dictionary['gtf'] = array_inputs_gtf
+    if array_inputs_blastxml:
+        all_datatype_dictionary['blastxml'] = array_inputs_blastxml
+    
+    print all_datatype_dictionary
+
+    for datatype, inputfiles in all_datatype_dictionary.items():
+        try:
+            user_input = inputfiles
+            if not user_input:
+                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)
+
+    jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory)
+    jbrowseHub.createHub()
+            
+            
+'''
+    if reference:
+        p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
+        # Wait for process to terminate.
+        p.communicate()
+    else:
+        parser.print_help()
+
+   
+    if input_simple_repeats:
+        bedToGff3(input_simple_repeats, chrom_size, 'trfbig', 'repeats.gff3')
+        label = "repeats"
+        p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'repeats.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
+        p.communicate()
+    if input_splice_junctions:
+        bedToGff3(input_splice_junctions, chrom_size, 'regtools', 'regtools.gff3')
+        label = "regtools"
+        p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'regtools.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
+        p.communicate()
+        attr = dict()
+        track = dict()
+        attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
+        track['regtools'] = attr
+        json_file = os.path.join(out_path, "trackList.json")
+        utils.add_tracks_to_json(json_file, track, 'add_attr')
+    if blastxml:
+        blastxmlToGff3.blastxml2gff3(blastxml, "blast.gff3")
+        label = "blast"
+        p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'blast.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
+        p.communicate()
+    if array_inputs_gff3:
+        for gff3 in array_inputs_gff3:
+            label = os.path.basename(gff3)
+            label = label.replace('.', '_')
+            p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', gff3, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
+            p.communicate()
+            if 'Augustus' in label:
+                attr = dict()
+                track = dict()
+                attr['transcriptType'] = 'transcript'
+                track['Augustus'] = attr
+                json_file = os.path.join(out_path, "trackList.json")
+                utils.add_tracks_to_json(json_file, track, 'add_attr')
+    if bam:
+        json_file = os.path.join(out_path, "trackList.json")
+        bam_track = dict()
+        bam_track['type'] = 'JBrowse/View/Track/Alignments2'
+        bam_track['label'] = 'alignments'
+        bam_track['urlTemplate'] = '../raw/HISAT_on_data_3,_data_2,_and_data_1.bam'
+        utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
+        print "add bam track\n"
+    if bigwig:
+        json_file = os.path.join(out_path, "trackList.json")
+        bigwig_track = dict()
+        bigwig_track['label'] = 'rnaseq'
+        bigwig_track['key'] = 'RNA-Seq Coverage'
+        bigwig_track['urlTemplate'] = '../raw/Convert_Bam_to_BigWig_on_data_3_and_data_15.bigwig'
+        bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
+        bigwig_track['variance_band'] = True
+        bigwig_track['style'] = dict()
+        bigwig_track['style']['pos_color'] = '#FFA600'
+        bigwig_track['style']['neg_color'] = '#005EFF'
+        bigwig_track['style']['clip_marker_color'] = 'red'
+        bigwig_track['style']['height'] = 100
+        utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
+    
+    if gtf:
+        utils.gtfToGff3(gtf, 'stringtie.gff3', chrom_size)
+        label = os.path.basename('stringtie')
+        p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'stringtie.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
+        p.communicate()
+        attr = dict()
+        track = dict()
+        attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
+        track['stringtie'] = attr
+        json_file = os.path.join(out_path, "trackList.json")
+        utils.add_tracks_to_json(json_file, track, 'add_attr')
+        
+    # Index name, it takes a long time, exclude it for now
+    p = subprocess.Popen(['JBrowse-1.12.1/bin/generate-names.pl', '-v', '--out', out_path])
+    p.communicate()
+    print "finished name index \n"
+'''
+
+if __name__ == "__main__":
+    main(sys.argv)
+