Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
linked reads molecule ordering
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container Registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Yoann DUFRESNE
linked reads molecule ordering
Commits
a304859c
Commit
a304859c
authored
5 years ago
by
Yoann Dufresne
Browse files
Options
Downloads
Patches
Plain Diff
main adaptation for threshold
parent
c9f90cbf
No related branches found
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
deconvolution/main/to_d2_graph.py
+2
-1
2 additions, 1 deletion
deconvolution/main/to_d2_graph.py
with
2 additions
and
1 deletion
deconvolution/main/to_d2_graph.py
+
2
−
1
View file @
a304859c
...
...
@@ -13,6 +13,7 @@ def parse_arguments():
parser
.
add_argument
(
'
--output_prefix
'
,
'
-o
'
,
default
=
"
d2_graph
"
,
help
=
"
Output file prefix.
"
)
parser
.
add_argument
(
'
--threads
'
,
'
-t
'
,
default
=
8
,
type
=
int
,
help
=
'
Number of thread to use for dgraph computation
'
)
parser
.
add_argument
(
'
--debug
'
,
'
-d
'
,
action
=
'
store_true
'
,
help
=
"
Debug
"
)
parser
.
add_argument
(
'
--edge_divergence_threshold
'
,
'
-dt
'
,
default
=
0.25
,
type
=
float
,
help
=
'
Divergence threshold value to link two udgs in the d2-graph
'
)
parser
.
add_argument
(
'
--maxclq
'
,
'
-c
'
,
action
=
'
store_true
'
,
help
=
"
Enable max clique community detection (default behaviour)
"
)
parser
.
add_argument
(
'
--louvain
'
,
'
-l
'
,
action
=
'
store_true
'
,
help
=
"
Enable Louvain community detection instead of all max-cliques
"
)
parser
.
add_argument
(
'
--comtest
'
,
'
-k
'
,
action
=
'
store_true
'
,
help
=
"
Enable [placeholder] community detection algorithm instead of max-cliques
"
)
...
...
@@ -64,7 +65,7 @@ def main():
d2g
=
d2
.
D2Graph
(
G
,
debug
=
debug
,
debug_path
=
debug_path
)
dprint
(
"
D2 graph object created
"
)
dprint
(
"
constructing d2 graph from barcode graph
"
)
d2g
.
construct_from_barcodes
(
neighbor_threshold
=
d2
_threshold
,
clique_mode
=
clique_mode
,
threads
=
args
.
threads
)
d2g
.
construct_from_barcodes
(
neighbor_threshold
=
args
.
edge_divergence
_threshold
,
clique_mode
=
clique_mode
,
threads
=
args
.
threads
)
dprint
(
"
[debug] d2 graph constructed
"
)
# d2g.save(f"{args.output_prefix}.tsv")
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
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!
Save comment
Cancel
Please
register
or
sign in
to comment