From c2cfe0701c63899f8ed35ef3cab08cbfdc84f2de Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 29 Oct 2020 16:52:23 +0100
Subject: [PATCH] src/find_interaction_cluster/nt_and_community.py: add a
region parameter
---
.../nt_and_community.py | 23 ++++++++++++++-----
1 file changed, 17 insertions(+), 6 deletions(-)
diff --git a/src/find_interaction_cluster/nt_and_community.py b/src/find_interaction_cluster/nt_and_community.py
index 48896d40..3f769be1 100644
--- a/src/find_interaction_cluster/nt_and_community.py
+++ b/src/find_interaction_cluster/nt_and_community.py
@@ -27,13 +27,14 @@ from .sf_and_communities import get_key
def get_nt_frequency(cnx: sqlite3.Connection, list_ft: List[str],
- feature: str) -> pd.DataFrame:
+ feature: str, region: str = "") -> pd.DataFrame:
"""
Get the frequency of every nucleotides for features in list_ft.
:param cnx: Connection to chia-pet database
:param list_ft: The list of exons for which we want to get
:param feature: the kind of feature analysed
+ :param region: The region of gene analysed if feature is gene
:return: the frequency of nucleotides for the list of exons.
>>> d = get_nt_frequency(sqlite3.connect(ConfigGraph.db_file),
@@ -49,13 +50,18 @@ def get_nt_frequency(cnx: sqlite3.Connection, list_ft: List[str],
0 1 29.49376 18.34271 18.43874 33.72479
1 2 31.90401 16.40251 18.79033 32.90315
"""
+ query_region = ""
if feature == "gene":
list_ft = [int(ft) for ft in list_ft]
+ if region == "":
+ region = "gene"
+ query_region = f"AND region = '{region}'"
query = f"""
SELECT ft, id_{feature}, frequency
FROM cin_{feature}_frequency
WHERE id_{feature} IN {tuple(list_ft)}
AND ft_type="nt"
+ {query_region}
"""
df = pd.read_sql_query(query, cnx)
df = df.pivot_table(index=f"id_{feature}", columns="ft", values="frequency")\
@@ -190,7 +196,8 @@ def get_ft_id(cnx: sqlite3.Connection, feature: str = "exon") -> List[str]:
def create_ctrl_community(df: pd.DataFrame, outfile: Path,
- feature: str = 'exon') -> pd.DataFrame:
+ feature: str = 'exon', region: str = ""
+ ) -> pd.DataFrame:
"""
:param df: A dataframe containing the frequency of each feature in a \
community.
@@ -206,7 +213,7 @@ def create_ctrl_community(df: pd.DataFrame, outfile: Path,
ft_id = get_ft_id(cnx, feature)
list_ft = [cid for cid in ft_id
if cid not in df[f"id_{feature}"].to_list()]
- df_nt = get_nt_frequency(cnx, list_ft, feature)
+ df_nt = get_nt_frequency(cnx, list_ft, feature, region)
df_com = get_community_table([list_ft], size_threshold, feature)
df_nt = df_nt.merge(df_com, how="left", on=f"id_{feature}")
df_nt['community'] = ['C-CTRL'] * df_nt.shape[0]
@@ -218,6 +225,7 @@ def create_ctrl_community(df: pd.DataFrame, outfile: Path,
def get_stat_nt_communities(df: pd.DataFrame, project: str, weight: int,
global_weight: int, same_gene: bool,
nt: str, feature: str = "exon",
+ region: str = "",
) -> pd.Series:
"""
Get data (proportion of `reg` regulated exons by a splicing factor
@@ -235,6 +243,7 @@ def get_stat_nt_communities(df: pd.DataFrame, project: str, weight: int,
same gene (True) or not (False) (default False)
:param nt: The nucleotide of interest
:param feature: The king of feature analysed
+ :param region: the region of interest to extract from gene
"""
logging.debug(f"lmm for {project}, w:{weight}, "
f"g:{global_weight} nt: {nt}")
@@ -254,7 +263,7 @@ def get_stat_nt_communities(df: pd.DataFrame, project: str, weight: int,
res['pval'] = pval
nt_ctrl_table = noutfile.parent / noutfile.name.replace("_stat.txt",
"_ctrl.txt")
- ndf = create_ctrl_community(df, nt_ctrl_table, feature)
+ ndf = create_ctrl_community(df, nt_ctrl_table, feature, region)
sum_df = lmm_maker_summary(ndf, outfile, nt)
outfile_ctrl = ConfigGraph.get_community_file(project, weight,
global_weight,
@@ -298,7 +307,7 @@ def create_dataframe(project: str, weight: int, global_weight: int,
def multiple_nt_lmm_launcher(ps: int, weights: List[int],
global_weights: List[int],
same_gene: bool,
- feature: str = 'exon',
+ feature: str = 'exon', region: str = '',
logging_level: str = "DISABLE"):
"""
Launch the statistical analysis for every
@@ -312,6 +321,7 @@ def multiple_nt_lmm_launcher(ps: int, weights: List[int],
:param same_gene: Say if we consider as co-localised exon within the \
same gene
:param feature: The kind of analysed feature
+ :param region: the region of interest to extract from gene
:param logging_level: Level of information to display
"""
ConfigGraph.community_folder.mkdir(exist_ok=True, parents=True)
@@ -342,7 +352,8 @@ def multiple_nt_lmm_launcher(ps: int, weights: List[int],
True)
df.to_csv(nfile_table, sep="\t", index=False)
dic_df[ckey] = df
- args = [df, project, weight, global_weight, same_gene, nt, feature]
+ args = [df, project, weight, global_weight, same_gene, nt, feature,
+ region]
if ckey not in processes.keys():
processes[ckey] = [pool.apply_async(get_stat_nt_communities, args)]
else:
--
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