From 97b8d4342467d6c280db97c808a8faa13b0d4274 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 28 Oct 2020 13:18:30 +0100
Subject: [PATCH] src/nt_composition/make_nt_correlation.py: modification of
get_project_colocalisation function by adding a parameter level
---
src/nt_composition/make_nt_correlation.py | 26 ++++++++++++++---------
1 file changed, 16 insertions(+), 10 deletions(-)
diff --git a/src/nt_composition/make_nt_correlation.py b/src/nt_composition/make_nt_correlation.py
index 2c94056c..ddbb5b18 100644
--- a/src/nt_composition/make_nt_correlation.py
+++ b/src/nt_composition/make_nt_correlation.py
@@ -61,9 +61,10 @@ 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) -> np.array:
+ inter_chr: bool = False,
+ level: str = "exon") -> np.array:
"""
- Get the interactions in project `project`
+ Get the interactions in project `project` for gene and exons
:param cnx: Connection to chia-pet database
:param project: The project of interest
@@ -78,22 +79,27 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
:param exon_bc: exons in big communities
:param inter_chr: True to only get inter-chromosomal interactions \
False else
+ :param the feature that we want to recover
:return: The table containing the number of interaction by projects
"""
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 ""
+ 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.")
+ same_gene = True
if exon_bc is None:
filter_exons = filter_exons_t = ''
else:
tmp = tuple(exon_bc)
- filter_exons = f' AND exon1 IN {tmp} AND exon2 IN {tmp}'
- filter_exons_t = f' AND t1.exon1 IN {tmp} AND t1.exon2 IN {tmp}'
+ filter_exons = f' AND {level}1 IN {tmp} AND {level}2 IN {tmp}'
+ filter_exons_t = f' AND t1.{level}1 IN {tmp} AND t1.{level}2 IN {tmp}'
if global_weight == 0:
if same_gene:
- query = f"SELECT exon1, exon2{select_add} " \
- "FROM cin_exon_interaction " \
+ query = f"SELECT {level}1, {level}2{select_add} " \
+ f"FROM cin_{level}_interaction " \
f"WHERE weight >= {weight} " \
f"AND id_project = '{project}'" \
+ filter_exons \
@@ -111,13 +117,13 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
else:
good_projects = tuple(ConfigNt.good_projects)
if same_gene:
- query = f"SELECT exon1, exon2{select_add} " \
- f"FROM cin_exon_interaction " \
+ query = f"SELECT {level}1, {level}2{select_add} " \
+ f"FROM cin_{level}_interaction " \
f"WHERE weight >= {weight} " \
f"AND id_project IN {good_projects} " \
f"{filter_exons} " \
f"{inter_str} " \
- f"GROUP BY exon1, exon2 " \
+ f"GROUP BY {level}1, {level}2 " \
f"HAVING COUNT(*) >= {global_weight}"
else:
query = f"""SELECT t1.exon1, t1.exon2{select_add}
@@ -134,7 +140,7 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
c = cnx.cursor()
c.execute(query)
- result = np.asarray(c.fetchall())
+ result = np.asarray(c.fetchall(), dtype=str)
if len(result) == 0:
msg = f'No interaction found in project {project}'
logging.exception(msg)
--
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