Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
L
LINcoding
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
Biodiversity and Epidemiology of Bacterial Pathogens
LINcoding
Commits
3576ef44
Commit
3576ef44
authored
7 years ago
by
Mélanie HENNART
Browse files
Options
Downloads
Patches
Plain Diff
Update README.md
parent
97688193
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
README.md
+7
-2
7 additions, 2 deletions
README.md
with
7 additions
and
2 deletions
README.md
+
7
−
2
View file @
3576ef44
...
...
@@ -63,18 +63,23 @@ If Database exist :
## Example
The directory example contains allelic profiles file of Elizabethkingia.
This file is download on the site following : http://bigsdb.pasteur.fr/elizabethkingia/elizabethkingia.html
It contains 183 allelic profiles of the bacteria Elizabethkingia, with 1546 loci.
Identifiants bacterial is in column 1-2 and all others is loci.
In the example folder, you have example files from the following command:
-
Create DataBase LIN :
```
bash
python LINcode.py
-i
BIGSdb.txt
-t
1-2
-l
3-
-b
1,20,
45,66
,80,9
0
,9
5,96,98,99
,100
python LINcode.py
-i
BIGSdb
_eliza
.txt
-t
1-2
-l
3-
-b
1
0
,20,
50
,80,9
5
,9
9.67,99.74,99.81,99.87,99.94
,100
.0
```
-
Update DataBase LIN :
```
bash
python LINcode.py
-i
new_Ecoli.txt
-r
BIGSdb
.lin
-t
1-2
-l
3-
python LINcode.py
-i
new_Ecoli.txt
-r
BIGSdb
_eliza.txt
-t
1-2
-l
3-
```
____________________________________________________________________________
__
_
...
...
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