diff TrackHub.py @ 5:e7c80e9b70ae draft

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

--- a/TrackHub.py	Fri Mar 10 14:57:36 2017 -0500
+++ b/TrackHub.py	Tue Mar 14 12:24:37 2017 -0400
@@ -6,28 +6,28 @@
 import subprocess
 import string
 import shutil
-from mako.lookup import TemplateLookup
+import tempfile
+
+#TODO: package JBrowse file conversion .pl files
 
 class TrackHub:
-    def __init__(self, inputFiles, reference, outputDirect, tool_dir):
-        self.input_files = inputFiles
-        self.out_path = outputDirect
+    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path):
+        self.input_files = inputFiles.tracks
+        self.outfile = outputDirect
+        self.outfolder = extra_files_path
+        self.out_path = os.path.join(extra_files_path, genome)
         self.reference = reference
         self.tool_dir = tool_dir
+        self.raw = os.path.join(self.out_path, 'raw')
+        self.json = os.path.join(self.out_path, 'json')
         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 not os.path.exists(self.out_path):
+                raise ValueError('the output folder has not been created')
             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)
+            os.makedirs(self.json)
         except OSError as e:
             print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
         else:
@@ -39,19 +39,21 @@
             self.addTrack(input_file)
         self.indexName()
         self.makeArchive()
-        shutil.rmtree(self.out_path)
+        #shutil.rmtree(self.out_path)
+        self.outHtml()
         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])
+            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
+            p = subprocess.Popen(['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)
-
+    #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
     def addTrack(self, track):
-        if track.dataType == 'bam':
+        if track['dataType'] == 'bam':
             json_file = os.path.join(self.json, "trackList.json")
             bam_track = dict()
             bam_track['type'] = 'JBrowse/View/Track/Alignments2'
@@ -59,7 +61,7 @@
             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':
+        elif track['dataType'] == 'bigwig':
             json_file = os.path.join(self.json, "trackList.json")
             bigwig_track = dict()
             bigwig_track['label'] = 'rnaseq'
@@ -74,28 +76,45 @@
             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])
+            gff3_file = os.path.join(self.raw, track['fileName'])
+            label = track['fileName']
+            if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':
+                p = subprocess.Popen(['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(['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(['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 = subprocess.Popen(['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 = subprocess.Popen(['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)
-            
-        
-        
-        
+        shutil.make_archive(self.out_path, 'zip', self.out_path)  
+        shutil.rmtree(self.out_path) 
+    
+    def outHtml(self):
+        #htmloutput = tempfile.NamedTemporaryFile(self.outfile, suffix = '.html', bufsize=0, delete=False)
+        with open(self.outfile, 'w') as htmlfile:
+            htmlstr = 'The JBrowse Hub is created: <br>'
+            zipfiles = '<li><a href = "%s">Download</a></li>'
+            filedir_abs = os.path.abspath(self.outfile)
+            filedir = os.path.dirname(filedir_abs)
+            filedir = os.path.join(filedir, self.outfolder)
+            for root, dirs, files in os.walk(filedir):
+                for file in files:
+                    if file.endswith('.zip'):   
+                        relative_directory = os.path.relpath(root, filedir)
+                        relative_file_path = os.path.join(relative_directory, file)
+                        htmlstr += zipfiles % relative_file_path
+            #htmlstr = htmlstr % zipfile
+            htmlfile.write(htmlstr)
 
+   
+
+
+