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bis-aria
ariaec
Commits
92f7149b
Commit
92f7149b
authored
May 18, 2016
by
Fabrice Allain
Browse files
syntax modifications (report file name)
parent
a2908521
Changes
5
Hide whitespace changes
Inline
Side-by-side
ariaec/commands.py
View file @
92f7149b
...
...
@@ -79,7 +79,7 @@ class AriaEcCommand:
u
"restraints toolbox"
,
formatter_class
=
argp
.
ArgumentDefaultsHelpFormatter
)
parser
.
add_argument
(
"-o"
,
"--output"
,
dest
=
"output_directory"
,
type
=
str
,
help
=
"Output directory"
)
type
=
str
,
help
=
"Output directory"
,
required
=
True
)
parser
.
add_argument
(
"-c"
,
"--conf"
,
action
=
ReadableFile
,
dest
=
"conf_file"
,
default
=
None
,
help
=
"configuration file"
)
parser
.
add_argument
(
"--nolog"
,
action
=
"store_true"
,
...
...
ariaec/maplot.py
View file @
92f7149b
...
...
@@ -127,7 +127,7 @@ class AriaEcContactMap(object):
for
mapname
,
mapt
,
mapath
in
self
.
allresmap
.
keys
():
prefix
=
"_"
.
join
((
mapname
,
self
.
refname
))
prefix
=
"_"
.
join
((
mapname
,
self
.
refname
))
.
replace
(
"."
,
"_"
)
if
mapname
==
self
.
refname
:
if
not
self
.
settings
.
contactmap
.
args
.
get
(
"onlyreport"
,
False
):
...
...
ariaec/protmap.py
View file @
92f7149b
...
...
@@ -312,8 +312,8 @@ class ProteinMap(Map):
def
report
(
self
,
cmpmap
,
scoremap
=
None
,
outprefix
=
""
,
outdir
=
""
,
plotdir
=
""
,
plot_ext
=
"pdf"
,
plotag
=
True
):
reportpath
=
"%s/%s.report"
%
(
outdir
,
outprefix
)
logger
.
info
(
"Generate report file (%s)"
%
reportpath
)
reportpath
=
"%s/%s.
map
report"
%
(
outdir
,
outprefix
)
logger
.
info
(
"Generate
map
report file (%s)"
%
reportpath
)
with
open
(
reportpath
,
'w'
)
as
reportf
:
y_true
=
list
(
self
.
values
.
astype
(
int
).
flat
)
y_pred
=
list
(
cmpmap
.
values
.
astype
(
int
).
flat
)
...
...
ariaec/test/__init__.py
View file @
92f7149b
"""
ARIA EC test module
"""
# TODO
# Essayer de faire au moins un test par fonction/methode
#
# setup.py
# - run
bin/ec2aria.py
View file @
92f7149b
...
...
@@ -6,10 +6,7 @@
"""
from
__future__
import
absolute_import
,
division
,
print_function
# TODO: PLMContact object
# TODO: PLMContactsList object
# TODO: replace all aria_ec ref into script name
# TODO: nc factor function
# TODO: Utiliser scikit-bio pour traiter les sequences biologiques
import
logging
...
...
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