Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
panacota
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
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
Amandine PERRIN
panacota
Commits
b074f0dc
Commit
b074f0dc
authored
5 years ago
by
Amandine PERRIN
Browse files
Options
Downloads
Patches
Plain Diff
add path to sequence formatted
parent
c00044d0
No related branches found
Branches containing commit
No related tags found
Tags containing commit
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
PanACoTA/annotate_module/prokka_prodigal_functions.py
+3
-2
3 additions, 2 deletions
PanACoTA/annotate_module/prokka_prodigal_functions.py
with
3 additions
and
2 deletions
PanACoTA/annotate_module/prokka_prodigal_functions.py
+
3
−
2
View file @
b074f0dc
...
...
@@ -31,7 +31,7 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
Parameters
----------
genomes : dict
{genome: [
name, g
path_
cu
t_gembase, size, nbcont,
l
90]}
{genome: [
gembase_name, path_to_origfile,
path_
spli
t_gembase,
g
size, nbcont,
L
90]}
threads : int
max number of threads that can be used
force : bool
...
...
@@ -126,7 +126,7 @@ def run_prokka(arguments):
Parameters
----------
arguments : tuple
(gpath, prok_folder, cores_annot, name, force, nbcont, q) with:
(gpath, prok_folder, cores_annot, name, force, nbcont,
small,
q) with:
* gpath: path and filename of genome to annotate
* prok_folder: path to folder where all prokka folders for all genomes are saved
...
...
@@ -134,6 +134,7 @@ def run_prokka(arguments):
* name: output name of annotated genome
* force: True if force run (override existing files), False otherwise
* nbcont: number of contigs in the input genome, to check prokka results
* small: used for prodigal, if sequences to annotate are small. Not used here
* q : queue where logs are put
Returns
...
...
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