diff --git a/Snakefile_d2 b/Snakefile_d2
index dd3ad73a932b28ffaac0f176abd91ed0a5f2284f..14c096a22701b995d836ec40ca20ce4a71b20f0c 100644
--- a/Snakefile_d2
+++ b/Snakefile_d2
@@ -1,7 +1,7 @@
import glob
WORKDIR = "snake_exec" if "workdir" not in config else config["workdir"]
-INPUT = ["snake_tests/simu_bar_n1000_d5_m2-dev0.gexf"] if "input" not in config else config["input"]
+INPUT = ["snake_tests/simu_bar_n10000_d5_m2-dev0.gexf"] if "input" not in config else config["input"]
if "," in INPUT:
if INPUT[0] == "[":
INPUT = INPUT[1:-1]
diff --git a/Snakefile_data_simu b/Snakefile_data_simu
index 5a4638dd8c81ba481248b87aca73e01fa8bb271f..318918e5e041ec6f2fbddcf39c88c4ef87b91a40 100644
--- a/Snakefile_data_simu
+++ b/Snakefile_data_simu
@@ -1,6 +1,6 @@
OUTDIR="snake_exec" if "outdir" not in config else config["outdir"]
-N=[1000] if "n" not in config else config["n"] # Number of molecule to simulate
+N=[10000] if "n" not in config else config["n"] # Number of molecule to simulate
D=[5] if "d" not in config else config["d"] # Average coverage of each molecule
M=[2] if "m" not in config else config["m"] # Average number of molecule per barcode
M_DEV=[0] if "m_dev" not in config else config["m_dev"] # Std deviation for merging number
diff --git a/deconvolution/d_graph.py b/deconvolution/d_graph.py
index de03bc0f2d5ebdb783bf9dc5a96b71d965d0ad54..c5eebf5efe02224b831d92185605d996a81b1493 100644
--- a/deconvolution/d_graph.py
+++ b/deconvolution/d_graph.py
@@ -258,7 +258,7 @@ def compute_all_max_d_graphs(graph, debug=False, clique_mode=None):
# further decompose! into necessarily 2 communities
community_as_graph = nx.Graph(graph.subgraph(comm))
if len(community_as_graph.nodes()) <= 2:
- cliques += [community_as_graph.nodes()]
+ cliques += [list(community_as_graph.nodes())]
else:
cliques += map(list,nx.community.asyn_fluidc(community_as_graph,2))
diff --git a/deconvolution/to_d2_graph.py b/deconvolution/to_d2_graph.py
index b233393e4b46e8c2c1c4218853aa633326b6419b..59ed95162d89a8ab92d7961b37f3e27938307938 100755
--- a/deconvolution/to_d2_graph.py
+++ b/deconvolution/to_d2_graph.py
@@ -53,7 +53,7 @@ def main():
d2g = d2.D2Graph(G)
dprint("D2 graph object created")
dprint("constructing d2 graph from barcode graph")
- index_size = 8 #if clique_mode is None else 3
+ index_size = 12 #if clique_mode is None else 3
d2g.construct_from_barcodes(index_size=index_size, debug=debug, clique_mode=clique_mode)
dprint("[debug] d2 graph constructed")
diff --git a/test_louvain.sh b/test_louvain.sh
index 813d1cc455734e05a19260f44713297bee12dc32..ee79f24d42bd5ee425f1ec7d02a36284c825d424 100755
--- a/test_louvain.sh
+++ b/test_louvain.sh
@@ -1,12 +1,14 @@
-rm -Rf snake_tests/simu_bar_n1000_d5_m2*
+prefix=simu_bar_n1000_d6_m2
+
+rm -Rf snake_tests/$prefix*
snakemake -s Snakefile_data_simu
snakemake -s Snakefile_d2
-mv snake_exec/simu_bar_n1000_d5_m2.tar.gz snake_tests/simu_bar_n1000_d5_m2.tar.gz
+mv snake_exec/$prefix.tar.gz snake_tests/$prefix.tar.gz
cd snake_tests
-tar xf simu_bar_n1000_d5_m2.tar.gz
+tar xf $prefix.tar.gz
cd ..
do_max_cliques=1
@@ -15,11 +17,11 @@ then
echo "max-cliques"
- python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified.gexf
+ python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified.gexf
- python deconvolution/d2_to_path.py snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified.gexf
+ python deconvolution/d2_to_path.py snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified.gexf
- python deconvolution/evaluate.py --type path --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf _path.gexf
+ python deconvolution/evaluate.py --type path --barcode_graph snake_tests/"$prefix"/"$prefix".gexf _path.gexf
fi
@@ -29,11 +31,11 @@ then
echo "louvain"
- python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified_louvain.gexf
+ python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified_louvain.gexf
- python deconvolution/d2_to_path.py snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified_louvain.gexf
+ python deconvolution/d2_to_path.py snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified_louvain.gexf
- python deconvolution/evaluate.py --type path --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf _path.gexf
+ python deconvolution/evaluate.py --type path --barcode_graph snake_tests/"$prefix"/"$prefix".gexf _path.gexf
fi
do_comtest=0
@@ -43,10 +45,10 @@ then
echo "******************************* Testing algorithm"
- python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified_comtest.gexf
+ python deconvolution/evaluate.py --type d2 --barcode_graph snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified_comtest.gexf
- python deconvolution/d2_to_path.py snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2_d2_simplified_comtest.gexf
+ python deconvolution/d2_to_path.py snake_tests/"$prefix"/"$prefix".gexf snake_tests/"$prefix"/"$prefix"_d2_simplified_comtest.gexf
- python deconvolution/evaluate.py --type path --barcode_graph snake_tests/simu_bar_n1000_d5_m2/simu_bar_n1000_d5_m2.gexf _path.gexf
+ python deconvolution/evaluate.py --type path --barcode_graph snake_tests/"$prefix"/"$prefix".gexf _path.gexf
fi