Command-line Arguments

This section summarizes arguments for the commands described in the other sections. Arguments with two dashes (--) indicate that they are optional arguments. All arguments of update_annotation are positional (i.e., required).

Arguments for recommend_annotation

Name	Type	Description	Default value
model	string	SBML model file	N/A
--cutoff	float (0.0 - 1.0)	match score cutoff	0.0
--optimize	string (y, yes)	optimizing predictions	no
--mssc	string (top or above)	match score selection criteria	top
--save	string (sbml or csv)	type of file to be saved	csv
--outfile	string	path to save file	upated model.xml / recommendations.csv

Arguments for recommend_species

Name	Type	Description	Default value
model	string	SBML model file	N/A
--species	string (one or more)	list of species IDs	all existing species
--min_len	integer	element filter (minimum length of name)	0
--cutoff	float (0.0 - 1.0)	match score cutoff	0.0
--mssc	string (top or above)	match score selection criteria	top
--outfile	string	path to save file	species_rec.csv

Arguments for recommend_reactions

Name	Type	Description	Default value
model	string	SBML model file	N/A
--reactions	string (one or more)	list of reaction IDs	all existing reactions
--min_len	integer	element filter (minimum number of components)	0
--cutoff	float (0.0 - 1.0)	match score cutoff	0.0
--mssc	string (top or above)	match score selection criteria	top
--outfile	string	path to save file	reaction_rec.csv

Arguments for update_annotation

Name	Type	Description	Default value
infile	string	path of the original model file	N/A
feedback	string	file with feedback (UPDATE ANNOTATION column)	N/A
outfile	string	path of the new file with updated annotations	N/A