lib/qiime/pycogent_backports/uclust.py

patch to allow gapopen and gapext penalties to be changed in uclust

--- lib/qiime/pycogent_backports/uclust.py   2011-06-07 21:34:23.000000000 +0100
+++ ../16s/Qiime-1.2.1/build/lib/qiime/pycogent_backports/uclust.py     2011-02-22 21:00:06.000000000 +0000
@@ -107,10 +107,6 @@
         '--optimal':FlagParameter('--',Name='optimal'),

         '--stable_sort':FlagParameter('--',Name='stable_sort'),
-
-        '--gapopen':ValuedParameter('--',Name='gapopen',Delimiter=' '),
-
-        '--gapext':ValuedParameter('--',Name='gapext',Delimiter=' '),
     }

     _suppress_stdout = False
@@ -435,12 +431,6 @@
     if subject_fasta_filepath: app.Parameters['--lib'].on(subject_fasta_filepath)
     if suppress_new_clusters: app.Parameters['--libonly'].on()
     if stable_sort: app.Parameters['--stable_sort'].on()
-
-    app.Parameters['--gapopen'].on("2")
-    app.Parameters['--gapext'].on("1")
-
-    import sys
-    print >>sys.stderr, "set gap parameters for uclust"

     app_result = app({'--input':fasta_filepath,'--uc':output_filepath})
     return app_result