Revert "Adds logging based on historic troubleshooting incidents. Cou…

…ld be expanded in the future based on future issues"

This reverts commit 13ccfc2.

Resolves #13

fatools/lib/fautil/cmds.py

@@ -140,7 +140,6 @@ def init_argparser(parser=None):
 
 
 def main(args):
-    cerr('***** Entering main in FATools *****')
 
     if args.verbose != 0:
         set_verbosity(args.verbose)
@@ -204,7 +203,6 @@ def main(args):
 
 
 def do_facmds(args, fsa_list, _params, dbh=None):
-    cerr('***** Entering do_facmds in FATools *****')
 
     if args.ladder_rfu_threshold >= 0:
         _params.ladder.min_rfu = args.ladder_rfu_threshold
@@ -288,16 +286,12 @@ def do_align( args, fsa_list, _params, f_bad_files, dbh ):
             fsa.align(_params)
             good_fsa.append( (fsa, fsa_index) )
         except LadderMismatchException:
-            cerr('***** LadderMismatchException: {} *****'.format(fsa))
-
             f_bad_files.write(("LadderMismatch: %s\n") % fsa.filename)
-
-    cerr('***** good_fsas: {} *****'.format(good_fsa))
+
     return good_fsa
 
 
 def do_call( args, fsa_list, params, dbh ):
-    cerr('***** Entering do_call *****')
 
     cerr('I: Calling non-ladder peaks...')
 
@@ -325,7 +319,6 @@ def do_normalize( args, fsa_list, params ):
     panel = Panel.get_panel(args.panel)
 
     ladder_means = panel.get_ladder_area_means(fsa_list)
-    cerr('***** ladder_means: {} *****'.format(ladder_means))
 
     # normalize areas for each FSA
     for (fsa, fsa_index) in fsa_list:
@@ -648,8 +641,6 @@ def open_fsa( args, _params ):
             os.makedirs('.fatools_caches/channels')
 
     if args.file:
-        cerr('***** Reading args.file *****')
-
         for fsa_filename in args.file.split(','):
             fsa_filename = fsa_filename.strip()
 
@@ -664,7 +655,6 @@ def open_fsa( args, _params ):
             index += 1
 
     elif args.infile:
-        cerr('***** Reading args.infile *****')
 
         with open(args.infile) as f:
             buf, delim = detect_buffer( f.read() )
@@ -701,8 +691,6 @@ def open_fsa( args, _params ):
                 index += 1
 
     elif args.indir:
-        cerr('***** Reading args.indir *****')
-
         import glob
         for fsa_filename in sorted(glob.glob(args.indir+"/*.fsa")):
 
@@ -712,7 +700,6 @@ def open_fsa( args, _params ):
             fsa_list.append( (fsa, str(index)) )
             index += 1
 
-    cerr('***** fsa_list: {} *****'.format(fsa_list))
     return fsa_list
 
 

fatools/lib/fautil/mixin2.py

@@ -73,7 +73,6 @@ def get_alleles(self, broad_peaks_only=True):
 
     # ChannelMixIn scan method
     def scan(self, parameters):
-        cerr('***** Entering ChannelMixin.scan *****')
 
         if self.status != const.channelstatus.reseted:
             return
@@ -82,7 +81,6 @@ def scan(self, parameters):
 
 
     def preannotate(self, parameters):
-        cerr('***** Entering ChannelMixin.preannotate *****')
 
         params = parameters.ladder if self.is_ladder() else parameters.nonladder
 
@@ -92,8 +90,6 @@ def preannotate(self, parameters):
     # ChannelMixIn align method
     def align(self, parameters, ladder=None, anchor_pairs=None, saturated_peak_rtimes=[]):
         # sanity checks
-        cerr('***** Entering ChannelMixin.align *****')
-
         if self.marker.code != 'ladder':
             raise RuntimeError('E: align() must be performed on ladder channel!')
 
@@ -281,7 +277,6 @@ def create_channels(self, params):
 
     # FSAMixIn scan method
     def scan(self, parameters):
-        cerr('***** Entering FSAMixIn.scan *****')
 
         if self.scan_done: return
 
@@ -296,7 +291,6 @@ def scan(self, parameters):
 
     # FSAMixIn align method
     def align(self, parameters=None):
-        cerr('***** Entering FSAMixIn.align *****')
 
         self.scan(parameters)
 
@@ -305,7 +299,6 @@ def align(self, parameters=None):
 
     # FSAMixIn call method
     def call(self, parameters):
-        cerr('***** Entering FSAMixIn.call *****')
 
         if self.call_done: return
 
@@ -342,7 +335,6 @@ def get_ladder_channel(self):
 
         for c in self.channels:
             if c.marker.code == 'ladder':
-                cerr('***** get_ladder_channel: {} *****'.format(c))
                 return c
         raise RuntimeError('E: ladder channel not found')
 
@@ -450,7 +442,6 @@ def get_marker(self, dye):
 
 
     def get_ladder(self):
-        cerr('***** ladder: {} *****'.format(const.ladders[ self.data['ladder']]))
         return const.ladders[ self.data['ladder']]