Use chardet to auto-detect encoding from Pathway Tools terminal.

mpwt/pwt_wrapper.py

@@ -2,7 +2,7 @@
 Wrapping Pathway Tools for PathoLogic and attribute-values dat files creation.
 Move results files to an output folder.
 """
-
+import chardet
 import logging
 import os
 import shutil
@@ -133,7 +133,8 @@ def run_pwt(species_input_folder_path, patho_hole_filler, patho_operon_predictor
         # Check internal error of Pathway Tools.
         with open(pwt_log, 'w') as  pwt_writer:
             for patho_line in iter(patho_subprocess.stdout.readline, b''):
-                patho_line = patho_line.decode('ascii')
+                encoding = chardet.detect(patho_line)['encoding']
+                patho_line = patho_line.decode(encoding)
                 pwt_writer.write(patho_line)
                 if any(error in patho_line for error in errors):
                     logger.info('Error possibly with the genbank file.')
@@ -196,7 +197,8 @@ def run_pwt_dat(species_input_folder_path):
         load_subprocess = subprocess.Popen(cmd_dat, stdout=subprocess.PIPE, universal_newlines="")
         with open(dat_log, 'w') as  dat_file_writer:
             for load_line in iter(load_subprocess.stdout.readline, b''):
-                load_line = load_line.decode('ascii')
+                encoding = chardet.detect(load_line)['encoding']
+                load_line = load_line.decode(encoding)
                 dat_file_writer.write(load_line)
                 if any(dat_end in load_line for dat_end in dat_creation_ends):
                     load_subprocess.stdout.close()

setup.py

@@ -30,6 +30,7 @@
       packages=['mpwt'],
       install_requires=[
             'biopython>=1.70',
+            'chardet>=3.0.4'
             'docopt>=0.6.2',
             'gffutils>=0.9',
       ],