From fd031d72de9dd72cc38347803bae05bd27d2bb77 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Tue, 17 Nov 2020 15:12:48 +0100
Subject: [PATCH] src/find_interaction_cluster/create_ppi_files.py:
modification to call the new functions created in
src/find_interaction_cluster/radomization_test_ppi.py
---
src/find_interaction_cluster/create_ppi_files.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/find_interaction_cluster/create_ppi_files.py b/src/find_interaction_cluster/create_ppi_files.py
index 6be04f38..2e96d8e2 100644
--- a/src/find_interaction_cluster/create_ppi_files.py
+++ b/src/find_interaction_cluster/create_ppi_files.py
@@ -22,7 +22,7 @@ from .community_finder import create_graph, find_communities, \
write_cytoscape_graph
from doctest import testmod
from .radomization_test_ppi import get_ppi_community_gene, \
- get_dna_community_gene, update_overlap_df
+ get_dna_community_gene, update_overlap_df,summary_randomisation_test
def get_community_dic_fom_community_file(mfile: Union[Path, pd.DataFrame],
@@ -310,13 +310,23 @@ def ppi_stats_analysis(community_file: Path, fasterdb_ppi: Path,
ppi_gene = get_ppi_community_gene(pd.read_csv(ppi_outfile, sep="\t"))
dic_dna_gene = get_dna_community_gene(pd.read_csv(community_file,
sep="\t"))
- df = update_overlap_df(df_overlap, dic_dna_gene, ppi_gene, iteration)
+ df, dic_values = update_overlap_df(df_overlap, dic_dna_gene, ppi_gene,
+ iteration)
outstat = ConfigGraph.get_community_file(project, weight, global_weight,
same_gene, "gene",
f"ppi_gene_table_{iteration}_"
f"stat.txt",
"community_gene_vs_protein")
df.to_csv(outstat, sep="\t", index=False)
+ final_df = summary_randomisation_test(df, dic_dna_gene, ppi_gene,
+ iteration, dic_values,
+ use_seed = False)
+ outstat = ConfigGraph.get_community_file(project, weight, global_weight,
+ same_gene, "gene",
+ f"ppi_gene_table_{iteration}_"
+ f"stat_recap.txt",
+ "community_gene_vs_protein")
+ final_df.to_csv(outstat, sep="\t", index=False)
def ppi_stat_launcher(ps: int, weights: List[int],
--
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