From 34adf7327b9b6576003785fce09dd28e1c7b15fe Mon Sep 17 00:00:00 2001
From: Yoann Dufresne <yoann.dufresne0@gmail.com>
Date: Tue, 26 May 2020 11:41:19 +0200
Subject: [PATCH] README update
---
README.md | 16 ++++++++++++++++
Snakefile_d2_eval | 4 ++--
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 8444f79..c70b2a4 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,8 @@
A compilation of scripts and pipelines to count and extract scaffolds of barcodes from linked reads datasets.
+**WARNING**: This code is a proof of concept, not a usable software for production. If the code is too slow for your tests or you are encontering some bugs (maybe it's a feature ? :p) don't hesitate to contact us via the issues or with a direct mail to me (yoann [dot] dufresne [at] pasteur [dot] fr).
+
## Nomenclature warnings
During the process of writing a scientific article, some of the datastructure names have been modified.
In this repository the majority of the names are old names.
@@ -27,6 +29,20 @@ Install the package from the root directory.
For the majority of the scripts, argparse is used.
To know how to use it please use the -h command line option.
+### Test the complete pipeline on simulated data
+
+For a complete test, we made a bunch of snakemake files.
+If you are looking for a complete pipeline from synthetic data generation, you should look into the "Snakefile_d2_eval" file.
+You can play with the N (number of molecules in the interval graph), M (average number of merge to perform in a barcode), DEV (standard deviation on merge) variables to see impact on performances.
+These values are arrays. You can enter multiple values and all the combinations will be done.
+A summary is output in the tsv file "{WORKDIR}/eval_compare_maxclique.tsv.
+Warning: the pipeline can be very slow for huge number of parameters.
+
+Command to run the pipeline:
+```
+ snakemake -s Snakefile_d2_eval
+```
+
### Data simulation
* generate_fake_molecule_graph.py: Create a linear molecule graph, where the molecules are linked to the d molecules on their left and d molecules on their right.
diff --git a/Snakefile_d2_eval b/Snakefile_d2_eval
index e88cef7..6a7f1ec 100644
--- a/Snakefile_d2_eval
+++ b/Snakefile_d2_eval
@@ -3,8 +3,8 @@ include: "Snakefile_d2"
include: "Snakefile_d2_path"
WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
-N = [500]
-D = [6]
+N = [5000]
+D = [10]
M = [2]
DEV = [0]
--
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