logger fix on console , mbr folder in the --output_folder when specified

compomics · Jan 20, 2017 · ce26b6e · ce26b6e
1 parent a549742
commit ce26b6e
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Showing 3 changed files with 26 additions and 26 deletions.
diff --git a/moff.py b/moff.py
@@ -19,6 +19,7 @@
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 
+
 """
  input
    - MS2 ID file
@@ -87,7 +88,7 @@ def pyMZML_xic_out(name, ppmPrecision, minRT, maxRT, MZValue):
         return (pd.DataFrame(timeDependentIntensities, columns=['rt', 'intensity']), -1)
 
 
-def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output):
+def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output,log):
     # OS detect
     flag_windows = False
     if _platform in ["linux", "linux2", 'darwin']:
@@ -113,9 +114,6 @@ def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_outp
         # extract the name of the file
         name = name[0:start]
 
-    ch = logging.StreamHandler()
-    ch.setLevel(logging.ERROR)
-    log.addHandler(ch)
 
     if loc_output != '':
         if not (os.path.isdir(loc_output)):
@@ -158,6 +156,7 @@ def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_outp
 
     # read data from file
     data_ms2 = pd.read_csv(file_name, sep="\t", header=0)
+
     if not 'matched' in data_ms2.columns:
         # check if it is a PS file ,
         list_name = data_ms2.columns.values.tolist()
@@ -221,8 +220,6 @@ def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_outp
             log.warning('rt not found. Wrong matched peptide in the mbr step line: %i', c)
             c += 1
             continue
-
-        # convert rt to sec to min
         try:
             if flag_mzml:
                 # mzml raw file
@@ -378,11 +375,11 @@ def run_apex(file_name, raw_name, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_outp
     h_rt_w = args.rt_window
     s_w = args.rt_p_window
     s_w_match = args.rt_p_window_match
-    # if args.raw_list is not None:
-    #    raw_list = args.raw_list
-    # else:
-    #    raw_list = None
+
     loc_raw = args.raw
     loc_output = args.loc_out
-    # " init here the logger
-    run_apex(file_name, args.raw_list, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output)
+    # set stream option for logger
+    ch = logging.StreamHandler()
+    ch.setLevel(logging.ERROR)
+    log.addHandler(ch)
+    run_apex(file_name, args.raw_list, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output,log)
diff --git a/moff_all.py b/moff_all.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 
-import glob
 import argparse
+import logging
 import os
-import moff_mbr
+
 import moff
+import moff_mbr
 
-import logging
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 
@@ -100,8 +100,7 @@
 
 log.critical('Apex module ')
 c=0
-for file_name in mbr_list_loc: 
-	# glob.glob(folder + os.sep + "*.txt"):
+for file_name in mbr_list_loc:
     tol = args.toll
     h_rt_w = args.rt_window
     s_w = args.rt_p_window
@@ -113,5 +112,5 @@
 	raw_list = None
     loc_raw = args.raw
     loc_output = args.loc_out
-    moff.run_apex(file_name,raw_list ,tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output)
+    moff.run_apex(file_name,raw_list ,tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output,log)
     c+=1
diff --git a/moff_mbr.py b/moff_mbr.py
@@ -112,17 +112,22 @@ def run_mbr(args):
     log.addHandler(ch)
 
     if args.loc_in is None:
-        # output mbr_folder will be in the specified folder
-        output_dir = os.path.join('mbr_output')
-        #print output_dir
+        ## the user uses --inputtsv option
+        if  not (args.loc_out is None):
+            # if the user use --output_folder the mbr folder will be created there
+            output_dir = os.path.join(args.loc_out,'mbr_output')
+        else:
+             #  if the user does not use  --output_folder the mbr folder will be created on moFF path location
+            output_dir = os.path.join('mbr_output')
+            print os.path.abspath(output_dir)
 
     else:
+        ## the user use the --inputF option
         if os.path.exists(os.path.join(args.loc_in)):
             # if '/' in  str(args.loc_in):
             output_dir = os.path.join(args.loc_in, 'mbr_output')
         else:
-            exit(os.path.join(args.loc_in) + ' EXIT input folder path not well specified --> / missing ')
-
+            exit(os.path.join(args.loc_in) + ' EXIT input folder path is not well specified --> / missing or wrong path')
 
             # if not (os.path.isdir(args.loc_in)):
             #   exit(str(args.loc_in) + '-->  input folder does not exist ! ')
@@ -137,11 +142,10 @@ def run_mbr(args):
     #        exit(os.path.join(args.loc_in) + ' EXIT input folder path not well specified --> / missing ')
 
     if not (os.path.isdir(output_dir)):
-        log.critical("Created MBR output folder in : %s ", output_dir)
+        log.critical("Created MBR output folder in : %s ", os.path.abspath(output_dir))
         os.makedirs(output_dir)
     else:
-        log.critical("MBR Output folder in : %s ", output_dir)
-    # log.setLevel(logging.DEBUG)
+        log.critical("MBR Output folder in : %s ", os.path.abspath(output_dir))
     # set log to file
     w_mbr = logging.FileHandler(os.path.join(output_dir, args.log_label + '_mbr_.log'), mode='w')
     w_mbr.setLevel(logging.INFO)