Update main.py

Russel88 · Feb 19, 2024 · b4f5ef3 · b4f5ef3
1 parent abc0dbd
commit b4f5ef3
Showing 1 changed file with 0 additions and 4 deletions.
diff --git a/maginator/main.py b/maginator/main.py
@@ -73,16 +73,12 @@ def cli():
     app.add_argument('--min_length',help='Minimum number of aligned basepairs of a read to be included [%(default)s]', default=80, type=int)
     app.add_argument('--min_identity',help='Minimum percentage of identity for a read to be included [%(default)s]', default=95, type=int)	
     app.add_argument('--min_map', help='Minimum percentage of mapped bases for a read to be included [%(default)s]', default=80, type=int)
-    app.add_argument('--min_SG_genes', help='Minimum number of signature genes for a bin to be included [%(default)s]', default=3, type=int)
-    app.add_argument('--n_signature_genes',help='Number of signature genes used for the abundance matrix [%(default)s]', default=100, type=int)
     app.add_argument('--stat', help='Method employed to calculate the absolute abundances [%(default)s]', default='sum', type=str, choices=['sum', 't_avg','low_avg'])
     app.add_argument('--tail_percentage', help='Percentage range for the tail of the truncated mean or low_avg method [%(default)s]', default=25, type=float)
     app.add_argument('--min_gtdb_markers', help='Minimum GTDBtk marker genes shared between MGS and outgroup for rooting trees [%(default)s]', default=10, type=int)
     app.add_argument('--marker_gene_cluster_prevalence', help='Minimum prevalence of marker genes to be selected for rooting of MGS trees [%(default)s]', default=0.5, type=float)
-
     app.add_argument('--min_mapped_signature_genes', help='Minimum number of signature genes with reads mapped for the sample to be included in the refinement [%(default)s]', default=3, type=int)
     app.add_argument('--min_samples', help='Minimum number of samples containing the MAG cluster (more than "min_mapped_signature_genes" present) for the MAG cluster to identidy SG [%(default)s]', default=3, type=int)
-
     app.add_argument('--min_af', help='Minimim allele frequency for calling a base when creating phylogenies [%(default)s]', default=0.8, type=float)
     app.add_argument('--min_depth', help='Minimim read depth for calling a base when creating phylogenies [%(default)s]', default=2, type=int)
     app.add_argument('--min_nonN', help='Minimum fraction of non-N characters of a sample to be included in a phylogeny [%(default)s]', default=0.5, type=float)