From 6da5aa14bd19dc7ddc25cd89086593a5ffb31683 Mon Sep 17 00:00:00 2001
From: Yoann Dufresne <yoann.dufresne0@gmail.com>
Date: Tue, 6 Aug 2019 12:17:06 +0200
Subject: [PATCH] Description of the used scripts

---
 README.md | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index bc925be..ffe2cdc 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,24 @@
 
 Trying to deconvolve single tag assignment for multiple molecules
 
-## Run the deconvolution
+## Scripts
 
-    python3 src/deconvolve.py
+For the majority of the scripts, argparse is used.
+To know how to use it please use the -h option.
+
+### 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.
+
+* generate_fake_barcode_graph.py: Take a barcode graph as input (gexf formated) and outputs a barcode graph. The barcode graph is create by fusion of nodes from the molecule graph.
+
+### Data structures and algorithms
+
+* to_d2_graph.py: Mount a barcode graph into memory and create a d2 graph from it.
+
+* evaluate.py: take a d2 graph gexf file and and analyse it. Look for an approximation of the longest correct path to reconstruct a molecule graph. Take as input a d2 graph where the truth is known in the node names (the format used to create fake data).
+
+* analyse_d2_tsv.py: Take an tsv optimization file of a d2 graph and look for the variables coverage. Outputs the missing variables (if exists).
 
 ## Run the tests
 
-- 
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