Commit 55288e47 authored by Gerald Salin's avatar Gerald Salin
Browse files

in subsetAssignation.py : supress the sterrr, and redirect the message

to logging
parent f486c579
...@@ -16,6 +16,7 @@ ...@@ -16,6 +16,7 @@
# #
import os, sys import os, sys
import logging
from subprocess import Popen, PIPE from subprocess import Popen, PIPE
from jflow.utils import get_argument_pattern from jflow.utils import get_argument_pattern
...@@ -96,7 +97,7 @@ class SubsetAssignation (Analysis): ...@@ -96,7 +97,7 @@ class SubsetAssignation (Analysis):
self.use_index = "true" self.use_index = "true"
if not os.path.exists( self.databank + ".00.idx" ) : if not os.path.exists( self.databank + ".00.idx" ) :
self.use_index = "false" self.use_index = "false"
sys.stderr.write("[WARNING] " + self.__class__.__name__ + " works more quickly with megablast index.\n") logging.getLogger("SubsetAssignation").warn("would work more quickly with megablast index")
if group_prefix == None : if group_prefix == None :
self.add_parameter_list("group_prefixes", "group_prefix", default=list(map(os.path.basename, self.get_outputs('{basename_woext}', self.sequence_files)))) self.add_parameter_list("group_prefixes", "group_prefix", default=list(map(os.path.basename, self.get_outputs('{basename_woext}', self.sequence_files))))
......
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