Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Extend the removal of variants Y location to all that have existing X… #7

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
+13 −32
Open

Extend the removal of variants Y location to all that have existing X… #7

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 13 additions & 32 deletions bin/post_processing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,13 @@


class RemoveYDuplicates:
var2current = {}
ycoords2remove = {}
vars_list = set()
chr_x = 'X'
chr_y = 'Y'
columns_coords_list = ['current_varname','chr','start']
columns_coords = ','.join(columns_coords_list)
sqlite_query_sel = f"SELECT {columns_coords} FROM variant_coords WHERE chr='{chr_x}' or chr='{chr_y}';"
sqlite_query_del = f"DELETE FROM variant_coords WHERE current_varname=? and chr='{chr_y}' and start=?;"
var_col = 'current_varname'
sqlite_query_sel = f"SELECT DISTINCT {var_col} FROM variant_coords WHERE chr='{chr_x}' AND {var_col} IN (SELECT {var_col} FROM variant_coords WHERE chr='{chr_y}');"
sqlite_query_del = f"DELETE FROM variant_coords WHERE current_varname=? and chr='{chr_y}';"


def __init__(self,sqlite_file):
self.sqlite_file = sqlite_file
Expand All @@ -26,31 +25,14 @@ def get_current_var(self):
self.sqlite_cursor.execute(self.sqlite_query_sel)
variants = self.sqlite_cursor.fetchall()
for data in variants:
current_varname = data[0]
chr = data[1]
start = data[2]
if current_varname in self.var2current.keys():
self.var2current[current_varname][chr] = start
else:
self.var2current[current_varname] = { chr: start }


def filter_current_var(self):
for var in self.var2current.keys():
var_coords = self.var2current[var]
if self.chr_x in var_coords and self.chr_y in var_coords:
if var_coords[self.chr_x] == var_coords[self.chr_y]:
self.ycoords2remove[var] = var_coords[self.chr_y]
for v in self.ycoords2remove.keys():
print(f"- {v}: {self.ycoords2remove[v]}")
print(f"COUNT: {len(self.ycoords2remove.keys())}")


def remove_y_coords(self):
for var in self.ycoords2remove.keys():
start = self.ycoords2remove[var]
self.vars_list.add(data[0])
print(f"List of variants with coordinates on both X and Y: {','.join(self.vars_list)}")


def remove_extra_y_coords(self):
for var in self.vars_list:
try:
self.sqlite_cursor.execute(self.sqlite_query_del, (var,start))
self.sqlite_cursor.execute(self.sqlite_query_del, (var,))
self.sqlite_connection.commit()
except sqlite3.Error as e:
print(f"Failed to delete record in sqlite table: {e}")
Expand All @@ -69,8 +51,7 @@ def main():

current_var = RemoveYDuplicates(sqlite_file)
current_var.get_current_var()
current_var.filter_current_var()
#current_var.remove_y_coords()
current_var.remove_extra_y_coords()


if __name__ == '__main__':
Expand Down