From 889f393c27f9577e84017650d64b7c438a2aebbc Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Mon, 4 Oct 2021 12:10:53 +0100
Subject: [PATCH] Updated generating IGV scripts
---
NHS_WES_generate_DEC_IGV_aff_probands.py | 20 ++++++++++++--------
NHS_WES_generate_DEC_IGV_sib_from_quad.py | 20 ++++++++++++--------
2 files changed, 24 insertions(+), 16 deletions(-)
diff --git a/NHS_WES_generate_DEC_IGV_aff_probands.py b/NHS_WES_generate_DEC_IGV_aff_probands.py
index 25a965b..24f914f 100755
--- a/NHS_WES_generate_DEC_IGV_aff_probands.py
+++ b/NHS_WES_generate_DEC_IGV_aff_probands.py
@@ -12,7 +12,7 @@
# all G2P variants found in the individual VCF
#
# Author: MH
-# last modified: MAR 23, 2020
+# last modified: AUG 04, 2021
@@ -420,6 +420,7 @@ def read_G2P(in_file):
# go thru all of their variants
pro_vars = KIDS_G2P_DICT[pro_id] # a dict with keys: chr,start,end,ref,alt and values: (GT,gene_name,transcript)
for var_loc,var_info in pro_vars.iteritems():
+ var_chr,var_start,var_end,var_ref,var_alt = var_loc.split(':') #~#
found_in_all = True
# check if seen in all probands excl this one
@@ -429,13 +430,16 @@ def read_G2P(in_file):
found_in_all = False
break
- # if variant found, check if GT matches
+ # if variant found, check if GT matches (excl GT match requirement on chrX)
else:
- o_info = KIDS_G2P_DICT[o_id][var_loc]
- if var_info[0] != o_info[0]:
- print " Excluding variant %s in %s (GT = %s); it is seen in %s but GT does not match (ST = %s)" % (var_loc,pro_id,var_info[0],o_id,o_info[0])
- found_in_all = False
- break
+ if var_chr == 'chrX': #~#
+ pass #~#
+ else: #~#
+ o_info = KIDS_G2P_DICT[o_id][var_loc]
+ if var_info[0] != o_info[0]:
+ print " Excluding variant %s in %s (GT = %s); it is seen in %s but GT does not match (ST = %s)" % (var_loc,pro_id,var_info[0],o_id,o_info[0])
+ found_in_all = False
+ break
if found_in_all: # this variant has been found in all affected probands with matching GT, keep it
if var_loc not in SHARED_DICT: # it has not been recorded previously when considering another proband
@@ -459,7 +463,7 @@ def read_G2P(in_file):
new_key = '%s:%s:%s:%s' % (chr,start,ref,alt)
SHARED_DICT[new_key] = var_info
- print " Keeping %s found in all affected probands, same GT" % (new_key)
+ print " Keeping %s found in all affected probands, same GT (no check of GT match on chrX)" % (new_key)
print "---------------------"
diff --git a/NHS_WES_generate_DEC_IGV_sib_from_quad.py b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
index eb978f2..c0449e6 100755
--- a/NHS_WES_generate_DEC_IGV_sib_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
@@ -12,7 +12,7 @@
# all G2P variants found in the individual VCF
#
# Author: MH
-# last modified: SEPT 16, 2020
+# last modified: AUG 04, 2021
@@ -426,6 +426,7 @@ def read_G2P(in_file):
# go thru all of their variants
pro_vars = KIDS_G2P_DICT[pro_id] # a dict with keys: chr,start,end,ref,alt and values: (GT,gene_name,transcript)
for var_loc,var_info in pro_vars.iteritems():
+ var_chr,var_start,var_end,var_ref,var_alt = var_loc.split(':') #~#
found_in_all = True
# check if seen in all probands excl this one
@@ -435,13 +436,16 @@ def read_G2P(in_file):
found_in_all = False
break
- # if variant found, check if GT matches
+ # if variant found, check if GT matches (excl GT match requirement on chrX)
else:
- o_info = KIDS_G2P_DICT[o_id][var_loc]
- if var_info[0] != o_info[0]:
- print " Excluding variant %s in %s (GT = %s); it is seen in %s but GT does not match (ST = %s)" % (var_loc,pro_id,var_info[0],o_id,o_info[0])
- found_in_all = False
- break
+ if var_chr == 'chrX': #~#
+ pass #~#
+ else: #~#
+ o_info = KIDS_G2P_DICT[o_id][var_loc]
+ if var_info[0] != o_info[0]:
+ print " Excluding variant %s in %s (GT = %s); it is seen in %s but GT does not match (ST = %s)" % (var_loc,pro_id,var_info[0],o_id,o_info[0])
+ found_in_all = False
+ break
if found_in_all: # this variant has been found in all affected probands with matching GT, keep it
if var_loc not in SHARED_DICT: # it has not been recorded previously when considering another proband
@@ -465,7 +469,7 @@ def read_G2P(in_file):
new_key = '%s:%s:%s:%s' % (chr,start,ref,alt)
SHARED_DICT[new_key] = var_info
- print " Keeping %s found in all affected probands, same GT" % (new_key)
+ print " Keeping %s found in all affected probands, same GT (no check of GT match on chrX)" % (new_key)
print "---------------------"
--
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