diff blast.py @ 9:2bda64d39931 draft

Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.
author peterjc
date Wed, 26 Nov 2014 06:55:48 -0500
parents de11e1a921c4
children 5482a8cd0f36
line wrap: on
line diff
--- a/blast.py	Tue Jan 21 13:33:20 2014 -0500
+++ b/blast.py	Wed Nov 26 06:55:48 2014 -0500
@@ -3,7 +3,7 @@
 """
 
 from galaxy.datatypes.data import get_file_peek
-from galaxy.datatypes.data import Text, Data
+from galaxy.datatypes.data import Text, Data, GenericAsn1
 from galaxy.datatypes.xml import GenericXml
 from galaxy.datatypes.metadata import MetadataElement
 
@@ -180,8 +180,10 @@
             title = "This is a nucleotide BLAST database"
         elif self.file_ext =="blastdbp":
             title = "This is a protein BLAST database"
+        elif self.file_ext =="blastdbd":
+            title = "This is a domain BLAST database"
         else:
-            #Error?                                                                                                                                                                     
+            #Error?
             title = "This is a BLAST database."
         msg = ""
         try:
@@ -259,3 +261,22 @@
 #        self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
 #        self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
+
+
+class BlastDomainDb( _BlastDb, Data ):
+    """Class for domain BLAST database files."""
+    file_ext = 'blastdbd'
+    allow_datatype_change = False
+    composite_type = 'basic'
+
+    def __init__(self, **kwd):
+        Data.__init__(self, **kwd)
+        self.add_composite_file('blastdb.phr', is_binary=True)
+        self.add_composite_file('blastdb.pin', is_binary=True)
+        self.add_composite_file('blastdb.psq', is_binary=True)
+        self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
+        self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
+        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
+        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
+        self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
+        self.add_composite_file('blastdb.aux', is_binary=True, optional=True)