first pass cleanup of cistematic/genomes; change bamPreprocessing

[erange.git] / cistematic / genomes / __init__.py

diff --git a/cistematic/genomes/__init__.py b/cistematic/genomes/__init__.py
index 4dee9248836da4133204428fd6a476ad759ce8a4..81ba4ec2665ca7ef56cdfa03ebba5a096ce3333a 100644 (file)
--- a/cistematic/genomes/__init__.py
+++ b/cistematic/genomes/__init__.py
@@ -1,7 +1,7 @@
 ###########################################################################
 #                                                                         #
 # C O P Y R I G H T   N O T I C E                                         #
-#  Copyright (c) 2003-10 by:                                              #
+#  Copyright (c) 2003-13 by:                                              #
 #    * California Institute of Technology                                 #
 #                                                                         #
 #    All Rights Reserved.                                                 #
@@ -562,7 +562,7 @@ class Genome:
                 results.append((name, version, chromosome, start, stop, orientation, atype))
 
         # select all features on chromosome that have a "start" between start and stop
-        stmt = 'chromosome, start, stop, orientation, name, version, type from sequence_features where chromosome = "%s" and start >= %d and start <= %d %s order by start' % (chrom, qstart, qstop, featureClause)
+        stmt = 'select chromosome, start, stop, orientation, name, version, type from sequence_features where chromosome = "%s" and start >= %d and start <= %d %s order by start' % (chrom, qstart, qstop, featureClause)
         res = self.queryDB(stmt, fetchall=True)
         for entry in res:
             (chromosome, start, stop, orientation, name, version, atype) = entry