checked in Peter Slicker's patches for speeding up BLAST parser

under Python 2.3

Bio/File.py

@@ -34,15 +34,17 @@ def __init__(self, handle):
         self._saved = []
 
     def readlines(self, *args, **keywds):
-        lines = self._saved + apply(self._handle.readlines, args, keywds)
+        #lines = self._saved + apply(self._handle.readlines, args, keywds)
+        lines = self._saved + self._handle.readlines(*args,**keywds)
         self._saved = []
         return lines
 
     def readline(self, *args, **keywds):
         if self._saved:
             line = self._saved.pop(0)
         else:
-            line = apply(self._handle.readline, args, keywds)
+            #line = apply(self._handle.readline, args, keywds)
+            line = self._handle.readline(*args,**keywds)
         return line
 
     def read(self, size=-1):
@@ -80,7 +82,8 @@ def tell(self):
 
     def seek(self, *args):
         self._saved = []
-        apply(self._handle.seek, args)
+        ##apply(self._handle.seek, args)
+        self._handle.seek(*args)
 
     def __getattr__(self, attr):
         return getattr(self._handle, attr)

CONTRIB

@@ -26,6 +26,7 @@ Katharine Lindner <katel@worldpath.net>
 Tarjei Mikkelsen <tarjei@genome.wi.mit.edu>
 Mike Poidinger <Michael.Poidinger@eBioinformatics.com>
 Wolfgang Schueler <wolfgang@proceryon.at>
+Peter Slickers <piet@clondiag.com>
 Thomas Sicheritz-Ponten <thomas@cbs.dtu.dk>
 Thomas Rosleff Soerensen <rosleff@mpiz-koeln.mpg.de>
 Johann Visagie <wjv@cityip.co.za>