Commit 15c0ce69 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
Browse files

CHANGES IN DEFAULT PARAMETERS

- hybrids mode is now default. Use --hybrids-off to turn it off
- cutoffs now has a single default value: 0.3
- clans clustering is now activated by default. Use --clans-off to turn
it off
- clan_cutoff is now 0.3 0.7 (i.e. will use GCFs defined at 0.3 and will
form GCC using average distance between GCFs of 0.7 or less)
parent a59c1eb9
......@@ -1989,19 +1989,18 @@ def CMD_parser():
help="Classes that should NOT be included in the \
classification. E.g. \"--banned_classes PKSI PKSOther\"")
parser.add_argument("--cutoffs", dest="cutoffs", nargs="+", default=[0.10,
0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60,
0.65, 0.70, 0.75, 0.80], type=float, choices=[FloatRange(0.0,
1.0)], help="Generate networks using multiple raw distance \
parser.add_argument("--cutoffs", dest="cutoffs", nargs="+", default=[0.30],
type=float, choices=[FloatRange(0.0, 1.0)],
help="Generate networks using multiple raw distance \
cutoff values, example: --cutoffs 0.1, 0.25, 0.5, 1.0. Default: \
all values from 0.10 to 0.80 with 0.05 intervals.")
parser.add_argument("--clans", dest="clans",action="store_true",
default=False, help="BiG-SCAPE will perform a second \
parser.add_argument("--clans-off", dest="clans",action="store_false",
default=True, help="BiG-SCAPE will perform a second \
layer of clustering and attempt to group families \
assigned from clustering with cutoff of 0.5 to clans")
parser.add_argument("--clan_cutoff",dest="clan_cutoff",default=[0.5,0.8],
parser.add_argument("--clan_cutoff",dest="clan_cutoff",default=[0.3,0.7],
type=float, choices=[FloatRange(0.0, 1.0)],nargs=2,
help="Cutoff Parameters for which clustering families \
into clans will be performed in raw distance. First \
......@@ -2012,8 +2011,8 @@ def CMD_parser():
used for distances between families. Example: \
--clan_cutoff 0.5 0.8)")
parser.add_argument("--hybrids", dest="hybrids", action="store_true",
default=False, help="Toggle to also add BGCs with hybrid\
parser.add_argument("--hybrids-off", dest="hybrids", action="store_false",
default=True, help="Toggle to also add BGCs with hybrid\
predicted products from the PKS/NRPS Hybrids and Others\
classes to each subclass (e.g. a 'terpene-nrps' BGC from\
Others would be added to the Terpene and NRPS classes)")
......
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