NestedProkkaFix

Script to check for falsely split orthologues in roary outputs that use prokka annotation input

Usage

Nested_prokka_annotation_fix.py [-h] -o OUTPUT [-p PRESENCE_PERCEN] -r REFERENCE (-i ROARY_CSV | -id ROARY_WITH_DETAILS) (-gff INPUT_GFF_FOLDER | -dict GFF_DICTIONARY)

Parameters Description

options:

• h, --help : show this help message and exit
• o OUTPUT, --output OUTPUT: Output direcotry. (default: None)
• p PRESENCE_PERCEN, --presence_percen PRESENCE_PERCEN: Percentage of isolates a gene must be present. (default: 0.95)
• r REFERENCE, --reference REFERENCE: Reference accession. (default: None)
• i ROARY_CSV, --roary_csv ROARY_CSV: Roary presence and absence matrix. (default: None)
• id ROARY_WITH_DETAILS, --roary_with_details ROARY_WITH_DETAILS: Roary presence and absence matrix with annotationd details added. (default: None)
• gff INPUT_GFF_FOLDER, --input_gff_folder INPUT_GFF_FOLDER: path to folder containing all the prokka gff file (default: None)
• dict GFF_DICTIONARY, --gff_dictionary GFF_DICTIONARY: Preprocessed .JSON of GFF annotations. (default: None)