split-from-imgt.py: creates .fa files with some special sequences

Dd2 and Dd3 may play interesting roles.

germline/split-from-imgt.py

@@ -8,12 +8,22 @@ import sys
 open_files = {}
 current_file = None
 
+# Create isolated files for some sequences
+SPECIAL_SEQUENCES = [
+    'TRDD2*01',
+    'TRDD3*01',
+]
+
 for l in sys.stdin:
 
     if ">" in l:
         current_file = None
+        current_special = None
+
         if "Homo sapiens" in l and ("V-REGION" in l or "D-REGION" in l or "J-REGION" in l):
-            system = l.split('|')[1][:4]
+            seq = l.split('|')[1]
+            system = seq[:4]
+
             if system.startswith('IG') or system.startswith('TR'):
 
                 if system in open_files:
@@ -24,9 +34,15 @@ for l in sys.stdin:
                     current_file = open(name, 'w')
                     open_files[system] = current_file
 
+            if seq in SPECIAL_SEQUENCES:
+                name = '%s.fa' % seq.replace('*', '-')
+                print "  ==>", name
+                current_special = open(name, 'w')
+
 
     if current_file:
             current_file.write(l)
 
-
+    if current_special:
+            current_special.write(l)