Cole/fix status file name

.github/workflows/integration_tests.yml

@@ -46,7 +46,7 @@ jobs:
       with:
         repository: edilytics/CRISPResso2_tests
         token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }}
-        # ref: '<BRANCH-NAME>' # Use this to specify a branch other than master
+        ref: 'cole/add-file-prefix-to-batch' # Use this to specify a branch other than master
 
     - name: Run Basic
       run: |

CRISPResso2/CRISPRessoAggregateCORE.py

@@ -71,7 +71,7 @@ def main():
 
         parser.add_argument('--debug', help='Show debug messages', action='store_true')
         parser.add_argument('-v', '--verbosity', type=int, help='Verbosity level of output to the console (1-4), 4 is the most verbose', default=3)
-        
+
         # CRISPRessoPro params
         parser.add_argument('--use_matplotlib', action='store_true',
                         help='Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed')
@@ -98,7 +98,7 @@ def main():
 
         log_filename=_jp('CRISPRessoAggregate_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoAggregate_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoAggregate_status.json')))
 
         with open(log_filename, 'w+') as outfile:
               outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoBatchCORE.py

@@ -127,7 +127,7 @@ def main():
 
         log_filename = _jp('CRISPRessoBatch_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        status_handler = CRISPRessoShared.StatusHandler(_jp('CRISPRessoBatch_status.json'))
+        status_handler = CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoBatch_status.json'))
         logger.addHandler(status_handler)
 
         with open(log_filename, 'w+') as outfile:
@@ -398,7 +398,10 @@ def main():
         large_plot_cutoff = 300
 
         percent_complete_start, percent_complete_end = 90, 99
-        percent_complete_step = (percent_complete_end - percent_complete_start) / len(all_amplicons)
+        if all_amplicons:
+            percent_complete_step = (percent_complete_end - percent_complete_start) / len(all_amplicons)
+        else:
+            percent_complete_step = 0
         # report for amplicons
         for amplicon_index, amplicon_seq in enumerate(all_amplicons):
             # only perform comparison if amplicon seen in more than one sample

CRISPResso2/CRISPRessoCORE.py

@@ -1288,7 +1288,7 @@ def print_stacktrace_if_debug():
             with open(log_filename, 'w+') as outfile:
                 outfile.write('CRISPResso version %s\n[Command used]:\n%s\n\n[Execution log]:\n' %(CRISPRessoShared.__version__, crispresso_cmd_to_write))
 
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPResso_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_status.json')))
 
         aln_matrix_loc = os.path.join(_ROOT, "EDNAFULL")
         CRISPRessoShared.check_file(aln_matrix_loc)

CRISPResso2/CRISPRessoCompareCORE.py

@@ -142,7 +142,7 @@ def main():
 
         log_filename = _jp('CRISPRessoCompare_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoCompare_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoCompare_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\nCRISPRessoCompare %s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoMetaCORE.py

@@ -233,7 +233,7 @@ def main():
 
         log_filename=_jp('CRISPRessoMeta_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoMeta_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoMeta_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoPooledCORE.py

@@ -327,7 +327,7 @@ def main():
 
         log_filename = _jp('CRISPRessoPooled_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooled_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoPooled_status.json')))
 
         if args.zip_output and not args.place_report_in_output_folder:
             logger.warn('Invalid arguement combination: If zip_output is True then place_report_in_output_folder must also be True. Setting place_report_in_output_folder to True.')

CRISPResso2/CRISPRessoPooledWGSCompareCORE.py

@@ -231,7 +231,7 @@ def main():
 
         log_filename = _jp('CRISPRessoPooledWGSCompare_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooledWGSCompare_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoPooledWGSCompare_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write(

CRISPResso2/CRISPRessoShared.py

@@ -1856,9 +1856,11 @@ def check_custom_config(args):
                 custom_config['colors'] = config['colors']
 
             return custom_config
-        except Exception as e:
-            logger.warn("Cannot read json file '%s', defaulting config parameters." % args.config_file)
-            print(e)
+        except Exception:
+            if args.config_file:
+                logger.warn("Cannot read config file '%s', defaulting config parameters." % args.config_file)
+            else:
+                logger.warn("No config file provided, defaulting config parameters.")
     return config
 
 

CRISPResso2/CRISPRessoWGSCORE.py

@@ -347,7 +347,7 @@ def print_stacktrace_if_debug():
         except:
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoWGS_status.json')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoWGS_status.json')))
 
         info('Checking dependencies...')