ORForise 1.6.0__py3-none-any.whl → 1.6.1__py3-none-any.whl

ORForise/Aggregate_Compare.py

@@ -339,9 +339,7 @@ def comparator(options):
 
 
 def main():
-    print("Thank you for using ORForise\nPlease report any issues to: https://github.com/NickJD/ORForise/issues\n"
-          "Please Cite: https://doi.org/10.1093/bioinformatics/btab827\n"
-          "#####")
+    print(WELCOME)
 
     parser = argparse.ArgumentParser(description='ORForise ' + ORForise_Version + ': Aggregate-Compare Run Parameters.')
     parser._action_groups.pop()
@@ -350,7 +348,7 @@ def main():
 
     required.add_argument('-dna', dest='genome_dna', required=True, help='Genome DNA file (.fa) which both annotations '
                                                                     'are based on')
-    required.add_argument('-t', dest='tools', required=True, help='Which tools to analyse? (Prodigal,GeneMarkS)')
+    required.add_argument('-t', dest='tools', required=True, help='Which tools to analyse?')
     required.add_argument('-tp', dest='tool_predictions', required=True, help='Tool genome prediction file (.gff) - Provide'
                                                                          'file locations for each tool comma separated')
     required.add_argument('-ref', dest='reference_annotation', required=True,

ORForise/Annotation_Compare.py

@@ -11,10 +11,7 @@ try:
     from Comparator import tool_comparison
 except ImportError:
     from .Comparator import tool_comparison
-    from ORForise.utils import *
-
-
-
+    from .utils import *
 
 ##########################
 
@@ -165,8 +162,8 @@ def comparator(options):
 
 
             # Write metrics to CSV
-            with open(csv_file, 'w', newline='\n', encoding='utf-8') as out_file:
                 tool_out = csv.writer(out_file, quoting=csv.QUOTE_NONE, escapechar=" ")
+                tool_out = csv.writer(out_file, quoting=csv.QUOTE_NONE, escapechar=" ")  # type: ignore[arg-type]
                 tool_out.writerow(['Representative_Metrics:'])
                 tool_out.writerow(rep_metric_description.split(','))
                 tool_out.writerow([*rep_metrics])
@@ -261,7 +258,7 @@ def comparator(options):
 
 
 def main():
-    print("Thank you for using ORForise\nPlease report any issues to: https://github.com/NickJD/ORForise/issues\n#####")
+    print(WELCOME)
 
     parser = argparse.ArgumentParser(description='ORForise ' + ORForise_Version + ': Annotatione-Compare Run Parameters.')
     parser._action_groups.pop()
@@ -271,7 +268,7 @@ def main():
                                                                     'are based on')
     required.add_argument('-ref', dest='reference_annotation', required=True,
                         help='Which reference annotation file to use as reference?')
-    required.add_argument('-t', dest='tool', required=True, help='Which tool to analyse? (Prodigal)')
+    required.add_argument('-t', dest='tool', required=True, help='Which tool to analyse?')
     required.add_argument('-tp', dest='tool_prediction', required=True,
                         help='Tool genome prediction file (.gff) - Different Tool Parameters'
                              ' are compared individually via separate files')