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medema-group
BiG-SCAPE
Commits
e86a689d
Commit
e86a689d
authored
Feb 07, 2020
by
Jorge Navarro Muñoz
Browse files
Parameters: clarified '--clans-off' text
parent
72bd53c4
Changes
1
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Inline
Side-by-side
bigscape.py
View file @
e86a689d
...
...
@@ -2034,9 +2034,9 @@ def CMD_parser():
c=0.3."
)
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"
)
default
=
True
,
help
=
"
Toggle to deactivate
a second
\
layer of clustering
to
attempt to group families
\
in
to clans"
)
parser
.
add_argument
(
"--clan_cutoff"
,
dest
=
"clan_cutoff"
,
default
=
[
0.3
,
0.7
],
type
=
float
,
nargs
=
2
,
help
=
"Cutoff Parameters for which
\
...
...
@@ -2076,6 +2076,7 @@ def CMD_parser():
default
=
False
,
help
=
"Force domain prediction using
\
hmmscan even if BiG-SCAPE finds processed domtable files
\
(e.g. to use a new version of PFAM)."
)
parser
.
add_argument
(
"--skip_ma"
,
dest
=
"skip_ma"
,
action
=
"store_true"
,
default
=
False
,
help
=
"Skip multiple alignment of domains'
\
sequences. Use if alignments have been generated in a
\
...
...
@@ -2100,7 +2101,7 @@ def CMD_parser():
domain_whitelist.txt file"
,
default
=
False
,
action
=
"store_true"
)
parser
.
add_argument
(
"--version"
,
action
=
"version"
,
version
=
"%(prog)s 1.0 (2020-01-27)"
)
parser
.
add_argument
(
"--version"
,
action
=
"version"
,
version
=
"%(prog)s 1.0
.1
(2020-01-27)"
)
return
parser
.
parse_args
()
...
...
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