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just_prs.py
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just_prs.py
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from oakvar import BasePostAggregator
import sqlite3
from sqlite3 import Error
from pathlib import Path
import polars as pl
import urllib
SUM = "sum"
TOTAL = "total"
COUNT = "count"
TITLE = "title"
INVERS = "invers"
class CravatPostAggregator (BasePostAggregator):
prs: dict = {}
prs_names: list = []
# prs5_rsids = []
sql_get_prs: str = """SELECT name, title, total, invers FROM prs;"""
def check(self) -> bool:
return True
def setup(self) -> None:
self.sql_file:str = str(Path(__file__).parent) + "/data/prs.sqlite"
if Path(self.sql_file).exists():
self.prsconn:sqlite3.Connection = sqlite3.connect(self.sql_file)
self.prscursor:sqlite3.Cursor = self.prsconn.cursor()
self.prscursor.execute(self.sql_get_prs)
rows:tuple = self.prscursor.fetchall()
for row in rows:
self.prs_names.append(row[0])
self.prs[row[0]] = {SUM: 0, COUNT: 0, TITLE: row[1], TOTAL: int(row[2]), INVERS: int(row[3])}
sql_create:str = """ CREATE TABLE IF NOT EXISTS prs (
id integer NOT NULL PRIMARY KEY,
name text,
sum float,
avg float,
count int,
title text,
total int,
percent int,
fraction float,
invers text
)"""
self.result_path:Path = Path(self.output_dir, self.run_name + "_longevity.sqlite")
self.result_conn:sqlite3.Connection = sqlite3.connect(self.result_path)
self.result_cursor:sqlite3.Cursor = self.result_conn.cursor()
self.result_cursor.execute(sql_create)
self.result_conn.commit()
self.result_cursor.execute("DELETE FROM prs;")
def get_prs_dataframe(self, name: str) -> pl.DataFrame:
import platform
sql:str = f"SELECT pos, chrom, effect_allele, weight FROM prs, weights WHERE prs.name = '{name}' AND prs.id = weights.prsid"
ol_pl = platform.platform()
if ol_pl.startswith("Windows"):
conn_url = f"sqlite://{urllib.parse.quote(self.sql_file)}"
else:
conn_url = f"sqlite://{self.sql_file}"
return pl.read_database(sql, conn_url)
def save_debug_info(self, name, df1:pl.DataFrame, df2:pl.DataFrame):
df = df1.join(df2, how="outer", on="key")
df = df.select(['dbsnp__rsid', 'base__chrom', 'base__pos', "effect_allele", 'base__ref_base', 'base__alt_base', "weight"])
df = df.sort(by='dbsnp__rsid')
df.write_csv(Path(self.output_dir, "prs_debug_"+name+".tsv"), separator="\t")
def calculate_prs(self, data_df: pl.DataFrame, name: str) -> tuple:
prs_df:pl.DataFrame = self.get_prs_dataframe(name)
prs_df = prs_df.with_columns((pl.col('chrom') + pl.col('pos').cast(pl.datatypes.Utf8)).alias("key"))
unite:pl.DataFrame = data_df.join(prs_df, left_on='key', right_on="key")
unite1 = unite.filter(pl.col("A") == pl.col("effect_allele"))
unite2 = unite.filter(pl.col("B") == pl.col("effect_allele"))
self.save_debug_info(name, unite1, unite2)
res1:pl.Series = unite1.select(pl.col("weight")).sum()
res2:pl.Series = unite2.select(pl.col("weight")).sum()
#TODO: negative join for ref homo zygot
# anti_unite = prs_df.join(data_df, left_on="rsid", right_on="dbsnp__rsid", how="anti")
# res3 = anti_unite.filter(pl.col("effect_allele") == pl.col("ref")).select(pl.col("weight")).sum() * 2
return float(res1.item()) + float(res2.item()), unite.shape[0]
def process_file(self) -> None:
# self._close_db_connection()
data_df = self.get_df("variant", None, 0)
data_df = data_df.select(['base__pos', 'vcfinfo__zygosity', 'base__ref_base', 'base__alt_base', 'base__chrom', 'dbsnp__rsid'])
data_df = data_df.with_columns(pl.col('vcfinfo__zygosity').fill_null("het"))
data_df = data_df.with_columns((pl.col('base__chrom') + pl.col('base__pos').cast(pl.datatypes.Utf8)).alias("key"))
het_zygot = data_df.filter(pl.col('vcfinfo__zygosity') == 'het')
het_zygot = het_zygot.with_columns([pl.col('base__ref_base').alias("A"), pl.col('base__alt_base').alias("B")])
hom_zygot = data_df.filter(pl.col('vcfinfo__zygosity') == 'hom')
hom_zygot = hom_zygot.with_columns([pl.col('base__alt_base').alias("A"), pl.col('base__alt_base').alias("B")])
data_df = het_zygot.vstack(hom_zygot)
for name in self.prs_names:
sum, count = self.calculate_prs(data_df, name)
self.prs[name][SUM] = sum
self.prs[name][COUNT] = count
# self._open_db_connection()
def cleanup(self) -> None:
if self.result_cursor is not None:
self.result_cursor.close()
if self.result_conn is not None:
self.result_conn.commit()
self.result_conn.close()
if self.prscursor is not None:
self.prscursor.close()
if self.prsconn is not None:
self.prsconn.close()
# def annotate (self, input_data):
# rsid:str = str(input_data['dbsnp__rsid'])
# if rsid == '':
# return
#
# if not rsid.startswith("rs"):
# rsid = 'rs' + rsid
# alt:str = input_data['base__alt_base']
# ref:str = input_data['base__ref_base']
# chrom:str = input_data['base__chrom']
#
# query:str = f"SELECT prs.name, weights.weight, position.effect_allele FROM position, prs, weights WHERE chrom = '{chrom}'" \
# f" AND rsid = '{rsid}' AND weights.posid = position.id AND weights.prsid = prs.id"
#
# self.prscursor.execute(query)
# rows:tuple = self.prscursor.fetchall()
#
# if len(rows) == 0:
# return
#
# zygot:str = input_data['vcfinfo__zygosity']
# for name, weight, allele in rows:
# if not (allele == alt or (allele == ref and zygot == 'het')):
# continue
# weight:float = float(weight)
# if allele == alt and zygot == 'hom':
# weight = 2 * weight
#
# self.prs[name][SUM] += weight
# self.prs[name][COUNT] += 1
def get_percent(self, name:str, value:float) -> float:
sql_get_percent:str = f"SELECT 'min', percent, max(value) FROM percentiles, prs WHERE percentiles.prs_id = prs.id AND prs.name = '{name}' AND value <= {value} UNION " \
f"SELECT 'max', percent, min(value) FROM percentiles, prs WHERE percentiles.prs_id = prs.id AND prs.name = '{name}' AND value >= {value}"
self.prscursor.execute(sql_get_percent)
rows:tuple = self.prscursor.fetchall()
for row in rows:
if row[0] == 'min':
min_percent:float = row[1]
min_value:float = row[2]
if row[0] == 'max':
max_percent:float = row[1]
max_value:float = row[2]
if min_value is None:
return max_percent
if max_value is None:
return min_percent
if abs(min_value - value) > abs(max_value - value):
return max_percent
else:
return min_percent
def postprocess(self) -> None:
sql:str = """ INSERT INTO prs (name, sum, avg, count, title, total, percent, fraction, invers) VALUES (?,?,?,?,?,?,?,?,?);"""
for name in self.prs_names:
avg:float = 0
if self.prs[name][COUNT] > 0:
avg = self.prs[name][SUM] / (self.prs[name][COUNT] * 2)
percent:float = self.get_percent(name, self.prs[name][SUM])
if type(percent) is not float:
percent = 0.01
task:tuple = (name, self.prs[name][SUM], avg, self.prs[name][COUNT], self.prs[name][TITLE], self.prs[name][TOTAL], int(percent * 100),
percent, self.prs[name][INVERS])
self.result_cursor.execute(sql, task)