From 6f741c56d2b83d008b4889f5a2cf623b6ab3a4e3 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 25 Jun 2020 15:00:46 +0200
Subject: [PATCH] src/nt_composition/make_nt_correlation.py: creation of
get_select_addition and modification of get_project_colocalisation to get the
weight of the edges in the network if needed
---
src/nt_composition/make_nt_correlation.py | 43 ++++++++++++++++++-----
1 file changed, 35 insertions(+), 8 deletions(-)
diff --git a/src/nt_composition/make_nt_correlation.py b/src/nt_composition/make_nt_correlation.py
index 1ca00971..df1de4f2 100644
--- a/src/nt_composition/make_nt_correlation.py
+++ b/src/nt_composition/make_nt_correlation.py
@@ -16,7 +16,6 @@ import numpy as np
import doctest
from .config import ConfigNt
from ..logging_conf import logging_def
-from tqdm import tqdm
from typing import Dict, Tuple, Any, List
import seaborn as sns
import matplotlib.pyplot as plt
@@ -25,17 +24,41 @@ from itertools import product
from random import random
import multiprocessing as mp
import os
-from time import time
class NoInteractionError(Exception):
pass
+def get_select_addition(global_weight: int, get_weight: bool, same_gene: bool):
+ """
+ Return the column to add if get_weight is not false.
+
+ :param global_weight: The global weight to consider. if \
+ the global weight is equal to 0 then then density figure are calculated \
+ by project, else all projet are merge together and the interaction \
+ seen in `global_weight` project are taken into account
+ :param get_weight: Say if we want to recover the weight of the interaction
+ :param same_gene: Say if we consider as co-localised exon within the \
+ same gene
+ :return: The additional column to get
+ """
+ if get_weight:
+ if global_weight == 0 and same_gene:
+ return ', weight'
+ elif global_weight == 0 and not same_gene:
+ return ', t1.weight'
+ elif global_weight >= 0 and same_gene:
+ return ', AVG(weight)'
+ elif global_weight >= 0 and not same_gene:
+ return ', AVG(t1.weight)'
+ return ''
+
+
def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
weight: int,
- global_weight: int, same_gene: bool
- ) -> np.array:
+ global_weight: int, same_gene: bool,
+ get_weight: bool = False) -> np.array:
"""
Get the interactions in project `project`
@@ -46,17 +69,21 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
the global weight is equal to 0 then then density figure are calculated \
by project, else all projet are merge together and the interaction \
seen in `global_weight` project are taken into account
+ :param get_weight: Say if we want to recover the weight of the interaction
+ :param same_gene: Say if we consider as co-localised exon within the \
+ same gene
: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)
if global_weight == 0:
if same_gene:
- query = "SELECT exon1, exon2 " \
+ query = f"SELECT exon1, exon2{select_add} " \
"FROM cin_exon_interaction " \
f"WHERE weight >= {weight} " \
f"AND id_project = '{project}' "
else:
- query = f"""SELECT t1.exon1, t1.exon2
+ query = f"""SELECT t1.exon1, t1.exon2{select_add}
FROM cin_exon_interaction t1, cin_exon t2, cin_exon t3
WHERE t1.weight >= {weight}
AND id_project = '{project}'
@@ -65,13 +92,13 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
AND t2.id_gene != t3.id_gene"""
else:
if same_gene:
- query = f"SELECT exon1, exon2 " \
+ query = f"SELECT exon1, exon2{select_add} " \
f"FROM cin_exon_interaction " \
f"WHERE weight >= {weight} " \
f"GROUP BY exon1, exon2 " \
f"HAVING COUNT(*) >= {global_weight}"
else:
- query = f"""SELECT t1.exon1, t1.exon2
+ query = f"""SELECT t1.exon1, t1.exon2{select_add}
FROM cin_exon_interaction t1, cin_exon t2, cin_exon t3
WHERE t1.weight >= {weight}
AND t1.exon1 = t2.id
--
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