Get species from swissprot definition

Force creation of symbolic link in addinstance.

workflows/addinstance/__init__.py

@@ -86,7 +86,7 @@ class AddInstance (Workflow):
             subprocess.check_call( self.get_exec_path("sed") + " -i -e 's,^session\.connection.*,session.connection = jdbc:mysql://{host}:{port}/biomart_sessions?user={user}\&password={passwd},'  {propfile}".format( 
                                                                                   propfile = os.path.join( NGSPIPELINES_DIST, 'biomart.properties'), **ngs_reader.get_database_info() ), shell = True)
             #create link data
-            subprocess.check_call( self.get_exec_path("ln") + ' -s ' + os.path.join( instance_directory , 'data') + ' ' + os.path.join( NGSPIPELINES_DIST_PLUGIN, 'ngspipelines', 'public','ngspipelines' ) , shell = True)
+            subprocess.check_call( self.get_exec_path("ln") + ' -f -s ' + os.path.join( instance_directory , 'data') + ' ' + os.path.join( NGSPIPELINES_DIST_PLUGIN, 'ngspipelines', 'public','ngspipelines' ) , shell = True)
             if self.instance_url :
                 url = re.sub(r':\d+$', '', re.sub( r'\/$', '',  str(self.instance_url))) + ':' + str(self.instance_port)
                 if not url.startswith("http") :

workflows/rnaseqdenovo/bin/blast2annot.py

@@ -62,15 +62,7 @@ def spFromHit( alignment ):
       @param alignment : [Bio::blast::Record::Alignment] the alignment.
     """
     species = None
-    # GI
-    if re.match("gi\|\d+\|[^\|]+\|.+", alignment.hit_id) is not None:
-        try:
-            matches = re.search('\[([^\]]+)\]', alignment.hit_def)
-            species = matches.group(1)
-        except: # swissprot
-            pass
-    # GNL
-    elif re.match('gnl\|\w+\|\d+', alignment.hit_id) is not None:
+    if re.match(".*OS=.*", alignment.hit_def) is not None:
         try:
             matches = re.search("OS=([^=]+)", alignment.hit_def)
             if matches is not None:
@@ -79,13 +71,13 @@ def spFromHit( alignment ):
                 clean_matches = re.search("(.+) [A-Z][A-Z]$", species)
                 if clean_matches is not None:
                     species = clean_matches.group(1)
-            else:
-                matches = re.search('^gi\|\d+\|', alignment.hit_def)
-                if matches is not None:
-                    cross_references = re.split("gi\|\d+\|", alignment.hit_def )
-                    matches = re.search( '\[([^\]]+)\][^\[]*$', cross_references[1] )
-                    species = matches.group(1)
-        except: # ensembl
+        except: 
+            pass
+    else :                
+        try:
+            matches = re.search('\[([^\]]+)\]', alignment.hit_def)
+            species = matches.group(1)
+        except: 
             species = None
             pass
     # Others databases are not implemented