diff commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,38 @@
+"""
+Utility to handle a databank of HMM profiles.
+"""
+
+import sys
+from commons.pyRepetUnit.profilesDB.Profiles import Profiles
+from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank
+from commons.core.utils.FileUtils import FileUtils
+
+class ProfilesDatabankUtils:
+    """
+    Utility to handle a databank of HMM profiles.
+    """
+    
+    def read( inFileName, verbose=0 ):
+        """
+        Read a file in Pfam format and return a L[ProfilesDatabank<commons.core.ProfilesDatabank>} instance.
+        @param inFileName: name of the input file
+        @type inFileName: string
+        @param verbose: verbosity level
+        @type verbose: integer
+        """ 
+        if verbose > 0: print "reading file '%s'..." % ( inFileName ); sys.stdout.flush()
+        
+    
+        if FileUtils.isEmpty(inFileName):
+            return (None)
+        profilesInstance = Profiles() 
+        profilesDBInstance = ProfilesDatabank()
+        f = open( inFileName , "r")
+        while profilesInstance.read( f ):
+            profilesDBInstance.append( profilesInstance )
+            profilesInstance = Profiles()
+        f.close()
+        if verbose > 0: print "file '%s' is loaded" % ( inFileName ); sys.stdout.flush()
+        return (profilesDBInstance)
+    
+    read = staticmethod( read )