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medema-group
BiG-SCAPE
Commits
36fb0b23
Commit
36fb0b23
authored
Jun 04, 2019
by
Jorge Navarro Muñoz
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Bugfix:
- '--mibig', '--mibig13' and '--query_bgc' options are working again
parent
91e191c0
Changes
1
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4 deletions
+3
-4
bigscape.py
bigscape.py
+3
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bigscape.py
View file @
36fb0b23
...
...
@@ -2101,7 +2101,7 @@ def CMD_parser():
domain_whitelist.txt file"
,
default
=
False
,
action
=
"store_true"
)
parser
.
add_argument
(
"--version"
,
action
=
"version"
,
version
=
"%(prog)s 2019060
3
"
)
parser
.
add_argument
(
"--version"
,
action
=
"version"
,
version
=
"%(prog)s 2019060
4
"
)
return
parser
.
parse_args
()
...
...
@@ -2382,7 +2382,7 @@ if __name__=="__main__":
print
(
"
\n
Importing MIBiG files"
)
get_gbk_files
(
bgcs_path
,
output_folder
,
bgc_fasta_folder
,
int
(
options
.
min_bgc_size
),
include_gbk_str
,
exclude_gbk_str
,
bgc_info
)
[
'*'
]
,
exclude_gbk_str
,
bgc_info
)
for
i
in
genbankDict
.
keys
():
mibig_set
.
add
(
i
)
...
...
@@ -2400,8 +2400,7 @@ if __name__=="__main__":
else
:
print
(
"
\n
Importing query BGC file"
)
get_gbk_files
(
options
.
query_bgc
,
output_folder
,
bgc_fasta_folder
,
int
(
options
.
min_bgc_size
),
include_gbk_str
,
exclude_gbk_str
,
bgc_info
)
int
(
options
.
min_bgc_size
),
[
'*'
],
exclude_gbk_str
,
bgc_info
)
if
query_bgc
not
in
genbankDict
:
sys
.
exit
(
"Error: not able to include Query BGC (check valid classes, BGC size, etc. Run again with --verbose)"
)
...
...
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