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

ORForise/Convert_To_GFF.py

@@ -6,10 +6,10 @@ import sys
 
 try:
     from utils import *
-    from Tools.TabToGFF.TabToGFF import TabToGFF
+    from ORForise.src.ORForise.Aux.TabToGFF import TabToGFF
 except ImportError:
     from ORForise.utils import *
-    from ORForise.Tools.TabToGFF.TabToGFF import TabToGFF
+    from ORForise.Aux.TabToGFF.TabToGFF import TabToGFF
 
 
 def setup_logging(outdir, verbose=False):
@@ -71,19 +71,20 @@ def load_genome(genome_fasta):
 
 
 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 + ': Convert-To-GFF Run Parameters')
     parser._action_groups.pop()
 
     required = parser.add_argument_group('Required Arguments')
-    # Make genome DNA optional: if not provided we operate without genome sequence
-    required.add_argument('-dna', dest='genome_DNA', required=False, help='Genome DNA file (.fa)')
+
     required.add_argument('-i', dest='input_annotation', required=True, help='Input annotation file (tabular)')
     required.add_argument('-fmt', dest='format', required=True, help='Input format: blast, abricate, genemark')
     required.add_argument('-o', dest='output_dir', required=True, help='Output directory')
 
     optional = parser.add_argument_group('Optional Arguments')
+    # Make genome DNA optional: if not provided we operate without genome sequence
+    required.add_argument('-dna', dest='genome_DNA', required=False, help='Genome DNA file (.fa)')
     optional.add_argument('-gi', dest='gene_ident', default='CDS', required=False, help='Gene identifier types to extract (unused)')
     optional.add_argument('--verbose', dest='verbose', action='store_true', help='Verbose logging with logfile')