From 50acb5a3ceb87622d3798bee089aef385ac9c178 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 27 Nov 2020 15:23:47 +0100
Subject: [PATCH] src/find_interaction_cluster/__main__.py: modifications to
use the adapt functions
---
src/find_interaction_cluster/__main__.py | 22 +++++++++++++---------
1 file changed, 13 insertions(+), 9 deletions(-)
diff --git a/src/find_interaction_cluster/__main__.py b/src/find_interaction_cluster/__main__.py
index 797bfd86..37102fa6 100644
--- a/src/find_interaction_cluster/__main__.py
+++ b/src/find_interaction_cluster/__main__.py
@@ -13,15 +13,16 @@ from .config import ConfigGraph
from typing import List
from .install_hipMCL import install_hipmcl
from .sf_and_communities import multiple_stat_launcher
-from .nt_and_community import multiple_nt_lmm_launcher
+from .nt_and_community import multiple_nt_lm_launcher
from .create_ppi_files import ppi_stat_launcher
import logging
from ..logging_conf import logging_def
+from .colocalisation_n_ppi_analysis import coloc_ppi_stat_main
@lp.parse(weight=range(1, 11), global_weight=range(11),
feature=('gene', 'exon'), region=('', 'exon', 'intron', 'gene'),
- iteration="iteration > 20", test_type=('lmm', 'perm'),
+ iteration="iteration > 20", test_type=('lm', 'perm'),
component_type=("nt", "aa", "dnt"))
def launcher(weight: int = 1,
global_weight: int = 0,
@@ -29,7 +30,7 @@ def launcher(weight: int = 1,
ps: int = ConfigGraph.cpu,
html_fig: bool = False, feature: str = 'exon', region: str = '',
component_type: str = 'nt',
- iteration: int = 1000, test_type: str = "lmm",
+ iteration: int = 1000, test_type: str = "lm",
project: str = "GSM1018963_GSM1018964",
logging_level: str = "DISABLE"):
"""
@@ -68,13 +69,16 @@ def launcher(weight: int = 1,
html_fig, feature, logging_level)
multiple_stat_launcher(ps, weight, global_weight, project, same_gene,
feature, logging_level)
- multiple_nt_lmm_launcher(ps, weight, global_weight, project,
- same_gene, feature, region, component_type,
- test_type, iteration, logging_level)
+ multiple_nt_lm_launcher(ps, weight, global_weight, project,
+ same_gene, feature, region, component_type,
+ test_type, iteration, logging_level)
if feature == "gene":
- ppi_stat_launcher(weight, global_weight, project, same_gene,
- ConfigGraph.ppi_threshold, iteration,
- logging_level)
+ # ppi_stat_launcher(weight, global_weight, project, same_gene,
+ # ConfigGraph.ppi_threshold, iteration,
+ # logging_level)
+ coloc_ppi_stat_main(weight, global_weight, project, same_gene,
+ iteration, logging_level)
+
launcher()
\ No newline at end of file
--
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