diff --git a/src/nt_composition/make_nt_correlation.py b/src/nt_composition/make_nt_correlation.py
index 6af50f94e2c62bd23b984da0c63c8075ec52b238..0b2b82a5754c1d663ccf80368c2618fccedae5e8 100644
--- a/src/nt_composition/make_nt_correlation.py
+++ b/src/nt_composition/make_nt_correlation.py
@@ -25,7 +25,6 @@ from itertools import product
from random import random
import multiprocessing as mp
import os
-import re
class NoInteractionError(Exception):
@@ -34,7 +33,7 @@ class NoInteractionError(Exception):
def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
weight: int,
- global_weight: int,
+ global_weight: int, same_gene: bool
) -> np.array:
"""
Get the interactions in project `project`
@@ -50,16 +49,35 @@ def get_project_colocalisation(cnx: sqlite3.Connection, project: str,
"""
logging.debug(f'Recovering interaction ({os.getpid()})')
if global_weight == 0:
- query = "SELECT exon1, exon2 " \
- "FROM cin_exon_interaction " \
- f"WHERE weight >= {weight} " \
- f"AND id_project = '{project}' "
+ if same_gene:
+ query = "SELECT exon1, exon2 " \
+ "FROM cin_exon_interaction " \
+ f"WHERE weight >= {weight} " \
+ f"AND id_project = '{project}' "
+ else:
+ query = f"""SELECT t1.exon1, t1.exon2
+ FROM cin_exon_interaction t1, cin_exon t2, cin_exon t3
+ WHERE t1.weight >= {weight}
+ AND id_project = '{project}'
+ AND t1.exon1 = t2.id
+ AND t1.exon2 = t3.id
+ AND t2.id_gene != t3.id_gene"""
else:
- query = f"SELECT exon1, exon2 " \
- f"FROM cin_exon_interaction " \
- f"WHERE weight >= {weight} " \
- f"GROUP BY exon1, exon2 " \
- f"HAVING COUNT(*) >= {global_weight}"
+ if same_gene:
+ query = f"SELECT exon1, exon2 " \
+ 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
+ FROM cin_exon_interaction t1, cin_exon t2, cin_exon t3
+ WHERE t1.weight >= {weight}
+ AND t1.exon1 = t2.id
+ AND t1.exon2 = t3.id
+ AND t2.id_gene != t3.id_gene
+ GROUP BY exon1, exon2
+ HAVING COUNT(*) >= {global_weight}"""
c = cnx.cursor()
c.execute(query)
@@ -103,21 +121,6 @@ def get_all_exon_interacting_with_another(exon: str, arr: np.array,
return exons[exons != exon]
-def remove_exon_in_same_gene(prefix: str, oexon: np.array):
- """
- Remove all exons having the prefix `prefix` from `oexon`.
-
- :param prefix: A prefix
- :param oexon: The list of interacting exons
- :return: Removing all exon with the preifx in oexon
-
- >>> remove_exon_in_same_gene("19_",
- ... np.asarray(["1_5", "1_3", "19_1", "19_19", "3_3"]))
- array(['1_5', '1_3', '3_3'], dtype='<U5')
- """
- return oexon[np.nonzero(np.core.defchararray.find(oexon, prefix))]
-
-
def get_frequency_dic(cnx: sqlite3.Connection, ft: str, ft_type: str
) -> Dict[str, float]:
"""
@@ -149,7 +152,7 @@ def get_frequency_dic(cnx: sqlite3.Connection, ft: str, ft_type: str
def create_density_table(arr_interaction: np.array, dic_freq: Dict[str, float],
- analyse_id: str, same_gene: bool) -> pd.DataFrame:
+ analyse_id: str) -> pd.DataFrame:
"""
Create the density table, a table showing the frequency of \
a nucleotide in every exon in a chia-pet projet and the mean \
@@ -158,24 +161,16 @@ def create_density_table(arr_interaction: np.array, dic_freq: Dict[str, float],
:param arr_interaction: array of interaction between exons.
:param dic_freq: The frequency dataframe.
:param analyse_id The id of the current analysis
- :param same_gene: Say if we consider as co-localised exon within the \
- same gene
:return: The density table
"""
logging.debug(f'Calculating density table ({os.getpid()})')
exons_list = get_interacting_exon(arr_interaction)
dic = {'exon': [], 'freq_exon': [], 'freq_coloc_exon': [], 'oexon': []}
pbar = tqdm(exons_list, desc=f"Working on {analyse_id} ({os.getpid()}) :",
- position=mp.current_process()._identity[0] - 1)
- pat = None
- if not same_gene:
- pat = re.compile(r"_\d+")
+ position=mp.current_process()._identity[0] - 1, disable=None)
for exon in pbar:
freq_ex = dic_freq[exon]
oexon = get_all_exon_interacting_with_another(exon, arr_interaction)
- if not same_gene:
- prefix = re.sub(pat, '_', exon)
- oexon = remove_exon_in_same_gene(prefix, oexon)
freq_oexon = np.nanmean(np.asarray([dic_freq[ex] for ex in oexon],
dtype=float))
if freq_ex is not None and not np.isnan(freq_oexon):
@@ -257,11 +252,10 @@ def create_density_figure(nt: str, ft_type: str,
if not outfile.is_file():
cnx = sqlite3.connect(ConfigNt.db_file)
arr_interaction = get_project_colocalisation(cnx, project, weight,
- global_weight)
+ global_weight, same_gene)
dic_freq = get_frequency_dic(cnx, nt, ft_type)
analyse_id = f"{project}_{ft_type}_{nt}"
- df = create_density_table(arr_interaction, dic_freq, analyse_id,
- same_gene)
+ df = create_density_table(arr_interaction, dic_freq, analyse_id)
df.to_csv(outfile, sep="\t", index=False)
r, p = create_density_fig(df, project, ft_type, nt, weight,
global_weight)