Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
bis-aria
ariaec
Commits
57556cc5
Commit
57556cc5
authored
Feb 10, 2016
by
fabrice
Browse files
Flush before each maplot
parent
3108a9c6
Changes
11
Hide whitespace changes
Inline
Side-by-side
ariaec/commands.py
View file @
57556cc5
...
...
@@ -64,7 +64,13 @@ class AriaEcCommand:
def
_update_logger
(
self
,
log
):
if
log
and
hasattr
(
self
.
args
,
"output_directory"
):
log
.
set_outdir
(
self
.
args
.
output_directory
)
if
not
self
.
args
.
nolog
:
# Don't generate log files
# TODO: get handler list from json file or customlogging object
logger
.
removeHandler
(
"info_file_handler"
)
logger
.
removeHandler
(
"error_file_handler"
)
logger
.
removeHandler
(
"debug_file_handler"
)
log
.
set_outdir
(
self
.
args
.
output_directory
)
log
.
update_msg
(
self
.
args
.
command
)
log
.
welcome
()
...
...
@@ -76,6 +82,8 @@ class AriaEcCommand:
type
=
str
,
help
=
"Output directory"
)
parser
.
add_argument
(
"-c"
,
"--conf"
,
action
=
ReadableFile
,
dest
=
"conf_file"
,
default
=
None
,
help
=
"configuration file"
)
parser
.
add_argument
(
"--nolog"
,
action
=
"store_true"
,
default
=
False
,
help
=
"Don't generate log files"
)
# Create subcommands
self
.
_create_subparsers
(
parser
.
add_subparsers
(
dest
=
"command"
))
return
parser
...
...
@@ -173,6 +181,9 @@ class AriaEcCommand:
choices
=
self
.
contact_types
,
help
=
"Infile(s) "
"contact "
"type(s)"
)
parser
.
add_argument
(
"--merge"
,
nargs
=
"+"
,
dest
=
"merge"
,
choices
=
self
.
contact_types
,
help
=
"Merge given contact types with other maps"
)
parser
.
add_argument
(
"--nofilter"
,
dest
=
"nofilter"
,
action
=
"store_true"
,
default
=
None
,
help
=
"Do not use contact list "
"filter and select top n "
...
...
@@ -201,7 +212,6 @@ class AriaEcCommand:
if
self
.
args
.
output_directory
:
logger
.
info
(
"Updating output directory"
)
settings
.
infra
=
self
.
args
.
output_directory
settings
.
make_infra
()
return
settings
def
run
(
self
):
...
...
ariaec/commands.pyc
View file @
57556cc5
No preview for this file type
ariaec/conf/aria_ec.ini
View file @
57556cc5
...
...
@@ -61,7 +61,7 @@ cb_upper_bound: 7.0
; separated by "+" character [pos]. If empty, use only position
; filter (avoid short range restraints)
n_factor:
1.0
contactfilter:
pos
contactfilter:
all
conservation_treshold:
95
position_treshold:
5
nd_beta:
0.99
...
...
ariaec/ecsettings.py
View file @
57556cc5
...
...
@@ -148,9 +148,9 @@ class AriaEcSettings(Settings):
return
self
.
_scsc_min
def
make_infra
(
self
):
logger
.
info
(
"Making
infrastructure in %s"
%
self
.
outdir
)
logger
.
info
(
"Making
output directories"
)
for
direct
in
self
.
infra
:
logger
.
debug
(
"
Making
%s directory"
%
self
.
infra
[
direct
])
logger
.
debug
(
"
Create
%s directory"
%
self
.
infra
[
direct
])
if
not
os
.
path
.
exists
(
self
.
infra
[
direct
]):
os
.
makedirs
(
os
.
path
.
abspath
(
self
.
infra
[
direct
]))
...
...
ariaec/ecsettings.pyc
View file @
57556cc5
No preview for this file type
ariaec/maplot.py
View file @
57556cc5
...
...
@@ -33,6 +33,8 @@ class AriaEcContactMap(object):
indent
=
4
))
logger
.
debug
(
"Args:
\n
"
+
json
.
dumps
(
self
.
settings
.
contactmap
.
args
,
indent
=
4
))
if
not
self
.
settings
.
contactmap
.
args
.
get
(
"onlyreport"
,
False
):
self
.
settings
.
make_infra
()
# ----------------------------- Input -------------------------------- #
if
self
.
settings
.
contactmap
.
args
.
get
(
"prefix"
):
self
.
outprefix
=
"_"
.
join
((
get_filename
(
...
...
@@ -92,11 +94,27 @@ class AriaEcContactMap(object):
for
k
in
(
'size_fig'
,
'plot_ext'
,
'plot_dpi'
)}
outdir
=
self
.
settings
.
outdir
if
self
.
settings
.
contactmap
.
config
.
get
(
"save_fig"
):
if
self
.
settings
.
contactmap
.
config
.
get
(
"save_fig"
)
and
not
\
self
.
settings
.
contactmap
.
args
.
get
(
"onlyreport"
,
False
):
refmap
.
saveplot
(
outdir
=
outdir
,
outprefix
=
"_"
.
join
((
self
.
outprefix
,
"pdb"
)),
**
plotparams
)
if
self
.
settings
.
contactmap
.
args
.
get
(
"merge"
,
None
):
# Combine merge maps with other maps
mergelist
=
self
.
settings
.
contactmap
.
args
.
get
(
"merge"
)
for
mergetype
in
mergelist
:
if
mergetype
in
self
.
allresmap
:
mergemaps
=
self
.
allresmap
.
pop
(
mergetype
)
mergecontactmap
=
mergemaps
.
get
(
"contactmap"
)
for
mapt
in
self
.
allresmap
.
keys
():
if
mapt
!=
self
.
reftype
:
up_map
=
self
.
allresmap
[
mapt
][
"contactmap"
]
up_map
[:]
=
up_map
.
add
(
mergecontactmap
)
mergekey
=
"%s_%s"
%
(
mapt
,
mergetype
)
self
.
allresmap
[
mergekey
]
=
{}
self
.
allresmap
[
mergekey
][
"contactmap"
]
=
up_map
for
mapt
in
self
.
allresmap
.
keys
():
prefix
=
"_"
.
join
((
self
.
outprefix
,
mapt
,
self
.
reftype
))
...
...
@@ -139,7 +157,9 @@ class AriaEcContactMap(object):
outdir
=
outdir
,
plotag
=
not
self
.
settings
.
contactmap
.
args
.
get
(
"onlyreport"
),
plotdir
=
self
.
settings
.
infra
.
get
(
"graphics"
,
outdir
))
plotdir
=
self
.
settings
.
infra
.
get
(
"graphics"
,
outdir
)
if
not
self
.
settings
.
contactmap
.
args
.
get
(
"onlyreport"
)
else
self
.
settings
.
outdir
)
# Contact map comparison plot
# TODO: elementwise error with compare method
# Write cmp stats
...
...
ariaec/maplot.pyc
View file @
57556cc5
No preview for this file type
ariaec/protmap.py
View file @
57556cc5
...
...
@@ -69,11 +69,7 @@ class Map(pd.DataFrame):
self
.
sym
=
sym
self
.
desc
=
desc
@
staticmethod
def
plotflush
():
plt
.
clf
()
plt
.
cla
()
plt
.
close
()
def
sortedset
(
self
,
human_idx
=
False
):
# Remove duplicate in sort_list
...
...
@@ -190,13 +186,18 @@ class ProteinMap(Map):
def
sequence
(
self
):
raise
NotImplementedError
def
plotflush
(
self
):
plt
.
clf
()
plt
.
cla
()
plt
.
close
()
self
.
_maplot
=
None
@
property
def
maplot
(
self
):
# Contact map Plot
if
not
self
.
_maplot
:
# Flush matplot
logger
.
debug
(
"Build maplot"
)
self
.
plotflush
()
minticks
=
tickmin
(
self
,
shift
=
1
)
# Nb graduations
self
.
_maplot
=
sns
.
heatmap
(
self
,
square
=
True
,
cbar
=
False
,
...
...
@@ -636,7 +637,7 @@ class ResAtmMap(ProteinMap):
"Filtering values in matrix related to %s (%s)"
%
(
str
(
pair
),
str
(
treshold
)))
if
pair
in
((
"SC"
,
"SC"
),
(
"sc"
,
"sc"
)):
# Use scsc_min to apply treshold only for selected atom
# Use scsc_min to apply treshold
update
only for selected atom
# sidechain
idx_list
=
[]
col_list
=
[]
...
...
ariaec/protmap.pyc
View file @
57556cc5
No preview for this file type
ariaec/setup.py
View file @
57556cc5
...
...
@@ -48,6 +48,7 @@ class AriaEcSetup:
indent
=
4
))
logger
.
debug
(
"Args:
\n
"
+
json
.
dumps
(
self
.
settings
.
setup
.
args
,
indent
=
4
))
self
.
settings
.
make_infra
()
# -------------------------------------------------------------------- #
# ----------------------------- Input -------------------------------- #
# -------------------------------------------------------------------- #
...
...
ariaec/setup.pyc
View file @
57556cc5
No preview for this file type
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment