From 79bc55949775d35f86b94115199884bc3a1f9f71 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 29 Oct 2020 15:14:29 +0100
Subject: [PATCH] src/nt_composition/make_nt_correlation.py: add a distance
parameter into get_project_colocalisation function to recover only
interaction far from at least 10kb
---
src/nt_composition/make_nt_correlation.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/src/nt_composition/make_nt_correlation.py b/src/nt_composition/make_nt_correlation.py
index ddbb5b18..58969b9e 100644
--- a/src/nt_composition/make_nt_correlation.py
+++ b/src/nt_composition/make_nt_correlation.py
@@ -61,7 +61,7 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
global_weight: int, same_gene: bool,
get_weight: bool = False,
exon_bc: Optional[np.array] = None,
- inter_chr: bool = False,
+ inter_chr: bool = False, distance: int = 10000,
level: str = "exon") -> np.array:
"""
Get the interactions in project `project` for gene and exons
@@ -84,8 +84,11 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
"""
logging.debug(f'Recovering interaction ({os.getpid()})')
select_add = get_select_addition(global_weight, get_weight, same_gene)
- inter_str = " AND level = 'inter'" if inter_chr else ""
- inter_str_t = " AND t1.level = 'inter'" if inter_chr else ""
+ inter_str = " AND level = 'inter'" \
+ if inter_chr else f"AND (level = 'inter' OR distance >= {distance})"
+ inter_str_t = " AND t1.level = 'inter'" \
+ if inter_chr \
+ else f"AND (t1.level = 'inter' OR t1.distance >= {distance})"
if level == "gene" and not same_gene:
logging.warning(f"When level is equal to gene then same_gene must "
f"be true. Setting it to True.")
--
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