diff TrackHub.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/TrackHub.py	Fri Mar 10 13:48:19 2017 -0500
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+import os
+import trackObject
+import utils
+import subprocess
+import string
+import shutil
+from mako.lookup import TemplateLookup
+
+class TrackHub:
+    def __init__(self, inputFiles, reference, outputDirect, tool_dir):
+        self.input_files = inputFiles
+        self.out_path = outputDirect
+        self.reference = reference
+        self.tool_dir = tool_dir
+        try: 
+            if not self.out_path:
+                raise ValueError('empty output path\n')
+            if os.path.exists(self.out_path):
+                shutil.rmtree(self.out_path)
+            os.mkdir(self.out_path)
+            self.json = os.path.join(self.out_path, 'json')
+            if os.path.exists(self.json):
+                shutil.rmtree(self.json)
+            os.mkdir(self.json)
+            self.raw = os.path.join(self.out_path, 'raw')
+            if os.path.exists(self.raw):
+                shutil.rmtree(self.raw)
+            shutil.move('raw', self.out_path)
+        except OSError as e:
+            print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
+        else:
+            print "Create jbrowse folder {}".format(self.out_path)
+    
+    def createHub(self):
+        self.prepareRefseq()
+        for input_file in self.input_files:
+            self.addTrack(input_file)
+        self.indexName()
+        self.makeArchive()
+        shutil.rmtree(self.out_path)
+        print "Success!\n"
+    
+    def prepareRefseq(self):
+        try:
+            p = subprocess.Popen([os.path.join(self.tool_dir, 'prepare-refseqs.pl'), '--fasta', self.reference, '--out', self.json])
+            # Wait for process to terminate.
+            p.communicate()
+        except OSError as e:
+            print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
+
+    def addTrack(self, track):
+        if track.dataType == 'bam':
+            json_file = os.path.join(self.json, "trackList.json")
+            bam_track = dict()
+            bam_track['type'] = 'JBrowse/View/Track/Alignments2'
+            bam_track['label'] = track.fileName
+            bam_track['urlTemplate'] = os.path.join('../raw', track.fileName)
+            utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
+            print "add bam track\n"
+        elif track.dataType == 'bigwig':
+            json_file = os.path.join(self.json, "trackList.json")
+            bigwig_track = dict()
+            bigwig_track['label'] = 'rnaseq'
+            bigwig_track['key'] = 'RNA-Seq Coverage'
+            bigwig_track['urlTemplate'] = os.path.join('../raw', track.fileName)
+            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')
+        else: 
+            gff3_file = os.path.join(self.raw, track.fileName)
+            label = track.fileName
+            if track.dataType == 'bedSpliceJunctions' or track.dataType == 'gtf':
+                p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json])
+            elif track.dataType == 'gff3-transcript':
+                p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--config', '{"transcriptType": "transcript"}', '--out', self.json])
+            elif track.dataType == 'gff3':
+                p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--out', self.json])
+            else:
+                p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', self.json])
+            p.communicate()
+            
+    def indexName(self):
+        p = subprocess.Popen([os.path.join(self.tool_dir, 'generate-names.pl'), '-v', '--out', self.json])
+        p.communicate()
+        print "finished name index \n"
+
+    def makeArchive(self):
+        filename = os.path.basename(self.out_path)
+        shutil.make_archive(filename, 'tar', self.out_path)
+            
+        
+        
+        
+