Merge branch 'master' into debianized

[htsworkflow.git] / scripts / rerun_eland.py

diff --git a/scripts/rerun_eland.py b/scripts/rerun_eland.py
index c271970b3a4b5790cd2bdbb6bfdefb83e6fca743..af06cdd8919ebdda9ccb544532a22e6edf6dba44 100644 (file)
--- a/scripts/rerun_eland.py
+++ b/scripts/rerun_eland.py
@@ -6,8 +6,9 @@ import os
 import subprocess
 import sys
 
-from gaworkflow.pipeline import gerald
-from gaworkflow.pipeline import runfolder
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines.eland import extract_eland_sequence
+from htsworkflow.pipelines import runfolder
 
 def make_query_filename(eland_obj, output_dir):
     query_name = '%s_%s_eland_query.txt' 
@@ -40,7 +41,7 @@ def extract_sequence(inpathname, query_pathname, length, dry_run=False):
         try:
             instream = open(inpathname, 'r')
             outstream = open(query_pathname, 'w')
-            gerald.extract_eland_sequence(instream, outstream, 0, length)
+            extract_eland_sequence(instream, outstream, 0, length)
         finally:
             outstream.close()
             instream.close()