From 70b1933b8d934a9b1fcf805e9e55c9b373b1bb0f Mon Sep 17 00:00:00 2001
From: Tim Stickland <T.R.Stickland@gmail.com>
Date: Tue, 14 Aug 2018 16:08:12 +0100
Subject: [PATCH] fixed bug preventing proper logging ar levels lower than
 WARNING

---
 gffmunger/GFFMunger.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/gffmunger/GFFMunger.py b/gffmunger/GFFMunger.py
index fc167aa..3c85ac7 100644
--- a/gffmunger/GFFMunger.py
+++ b/gffmunger/GFFMunger.py
@@ -41,13 +41,17 @@ def __init__(self,options):
          
       # set up logger
       self.logger = logging.getLogger(__name__)
+      def setLogLevel(level):
+         self.logger.setLevel(level)
+         handler = logging.StreamHandler()
+         handler.setLevel(level)
+         self.logger.addHandler(handler)
       if self.verbose:
-         self.logger.setLevel(logging.INFO)
-         self.logger.warning("logging.debug & logging.info seem to be broken at the moment, you'll only see warnings & above :-/")
+         setLogLevel(logging.INFO)
       elif self.quiet:
-         self.logger.setLevel(logging.CRITICAL)
+         setLogLevel(logging.CRITICAL)
       else:
-         self.logger.setLevel(logging.WARNING)
+         setLogLevel(logging.WARNING)
 
       # options from configuration file
       config_filename = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', self.config_file)
@@ -109,9 +113,9 @@ def config_value_is_true(config_value):
          if self.output_file:
             self.output_file = None
          self.logger.debug("Writing output to STDOUT")
-      
 
-            
+
+
    def run(self):
       try:
          # get GFF3 input, stdin or file; sets self.gff3_input_filename
@@ -234,6 +238,8 @@ def validate_FASTA(self, fasta_filename, silent=False):
       Pass path of FASTA file; if valid, True is returned; if invalid, validator STDERR output is printed and False is returned
       Validation failure message printed to STDOUT; this can be supressed by passing the optional flag 'silent'"""
       self.logger.info("Validating FASTA file "+ fasta_filename)
+      if self.logger.isEnabledFor(logging.INFO):
+         print("*** logging INFO ***")
       with self.open_text_file(fasta_filename) as handle:
          fasta = SeqIO.parse(handle, "fasta")
          is_fasta = any(fasta)   # False when `fasta` is empty, i.e. wasn't a FASTA file
@@ -407,6 +413,8 @@ def move_annotations(self):
          modified_feature_cache.append(this_polypeptide)
                   
       self.logger.info("found "+str(num_polypeptide)+" polypeptide features")
+      if self.logger.isEnabledFor(logging.INFO):
+         print("*** logging INFO ***")
       
       self.check_for_anotations(modified_feature_cache)
       
@@ -532,6 +540,8 @@ def export_gff3(self):
          num_features_written+=1
          handle.write( str(this_feature)+"\n" )
       self.logger.info("extracted and wrote "+str(num_features_written)+" features from gffutils db")
+      if self.logger.isEnabledFor(logging.INFO):
+         print("*** logging INFO ***")
       
       # write fasta
       handle.write("##FASTA\n")