Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Open sidebar
VEBER Philippe
codepi
Commits
d93a3737
Commit
d93a3737
authored
Aug 24, 2018
by
Carine Rey
Browse files
check if input tree is rooted
parent
c92ad5ce
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
12 additions
and
4 deletions
+12
-4
lib/pipeline.ml
lib/pipeline.ml
+1
-1
lib/scripts/parse_input_tree.py
lib/scripts/parse_input_tree.py
+6
-0
lib/tree_dataset.ml
lib/tree_dataset.ml
+2
-2
lib/tree_dataset.mli
lib/tree_dataset.mli
+3
-1
No files found.
lib/pipeline.ml
View file @
d93a3737
...
...
@@ -121,7 +121,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
let
derive_from_tree
~
tree_dir
~
tree
~
profile
~
preview
~
use_concat
~
ns
~
no_Ne
~
no_HaPC
~
ne_test
=
let
tree_prefix
=
Filename
.
chop_extension
tree
in
let
input_tree
=
input
(
Filename
.
concat
tree_dir
tree
)
in
let
tree_dataset
=
Tree_dataset
.
prepare
input_tree
in
let
tree_dataset
=
Tree_dataset
.
prepare
~
descr
:
tree_prefix
input_tree
in
let
models
=
Convergence_hypothesis
.[
[
H0_NeG1
;
...
...
lib/scripts/parse_input_tree.py
View file @
d93a3737
...
...
@@ -105,6 +105,12 @@ if t:
features
=
list
(
set
(
features
))
# list(set(*)) = remove duplicates
logger
.
info
(
"No detected tag"
if
not
features
else
"Detected tags: "
+
", "
.
join
([
f
for
f
in
features
]))
#check rooted tree
nb_root_children
=
len
(
t
.
get_children
())
if
nb_root_children
>
2
:
logger
.
error
(
"Unrooted tree"
)
sys
.
exit
(
1
)
if
"ND"
in
features
:
logger
.
warning
(
"
\"
ND
\"
is in the detected tags but it will be removed by the programm"
)
features
.
remove
(
"ND"
)
...
...
lib/tree_dataset.ml
View file @
d93a3737
...
...
@@ -5,8 +5,8 @@ open File_formats
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
prepare
tree
=
workflow
~
descr
:
"utils.parse_input_tree
"
[
let
prepare
?
(
descr
=
""
)
tree
=
workflow
~
descr
:
(
"utils.parse_input_tree
."
^
descr
)
[
cmd
"python"
~
env
[
file_dump
(
string
Scripts
.
parse_input_tree
)
;
opt
"-t"
dep
tree
;
...
...
lib/tree_dataset.mli
View file @
d93a3737
open
Bistro
.
Std
open
File_formats
val
prepare
:
nhx
workflow
->
[
`tree_dataset
]
directory
workflow
val
prepare
:
?
descr
:
string
->
nhx
workflow
->
[
`tree_dataset
]
directory
workflow
val
nodes
:
[
`tree_dataset
]
directory
workflow
->
Convergence_hypothesis
.
t
->
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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