From e19e28e5108702fb97836dbcc3dc60cb9d863c20 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Fri, 18 Jun 2021 11:39:12 +0100
Subject: [PATCH] Update to handle different G2P output
---
NHS_WES_generate_DEC_IGV_aff_probands.py | 14 ++++++++------
NHS_WES_generate_DEC_IGV_sib_from_quad.py | 14 ++++++++------
2 files changed, 16 insertions(+), 12 deletions(-)
diff --git a/NHS_WES_generate_DEC_IGV_aff_probands.py b/NHS_WES_generate_DEC_IGV_aff_probands.py
index 29023d3..25a965b 100755
--- a/NHS_WES_generate_DEC_IGV_aff_probands.py
+++ b/NHS_WES_generate_DEC_IGV_aff_probands.py
@@ -349,27 +349,29 @@ def read_G2P(in_file):
##########################################
check_key = '%s:%s' % (sam_id,second_key)
- if check_key not in CHECK_DICT:
+ if check_key not in CHECK_DICT: # first time we see this var in this sample, any OBS_state
CHECK_DICT[check_key][OBS_state] = 1
if sam_id not in KIDS_G2P_DICT:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
elif second_key not in KIDS_G2P_DICT[sam_id]:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
- else:
- print "ERROR: should not be here: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
+ else: # sanity check
+ print "ERROR: first time var already seen?: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
raise SystemExit
- elif OBS_state not in CHECK_DICT[check_key].keys():
+ elif OBS_state not in CHECK_DICT[check_key].keys(): # first time we see this var in this sample with this OBS_state
CHECK_DICT[check_key][OBS_state] = 1
if sam_id not in KIDS_G2P_DICT:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
elif second_key not in KIDS_G2P_DICT[sam_id]:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
+ elif KIDS_G2P_DICT[sam_id][second_key] == (GT,gene_name,transcript): # diff OBS_state, but must have same (GT,gene_name,transcript)
+ pass
else:
- print "ERROR: should not be here: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
+ print "ERROR: diff (GT,gene_name,transcript) for variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
raise SystemExit
- else: # same individual, same variant, same OBS_state
+ else: # same individual, same variant, known OBS_state
# due to the new output of G2P we may have the same variant but with different gene names - ensembl/refseq
# check the gene name in KIDS_G2P_DICT[sam_id][second_key]
if not KIDS_G2P_DICT[sam_id][second_key][1].startswith('ENSG'): # recorded is refseq
diff --git a/NHS_WES_generate_DEC_IGV_sib_from_quad.py b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
index 304ceb7..eb978f2 100755
--- a/NHS_WES_generate_DEC_IGV_sib_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
@@ -354,27 +354,29 @@ def read_G2P(in_file):
##########################################
check_key = '%s:%s' % (sam_id,second_key)
- if check_key not in CHECK_DICT:
+ if check_key not in CHECK_DICT: # first time we see this var in this sample, any OBS_state
CHECK_DICT[check_key][OBS_state] = 1
if sam_id not in KIDS_G2P_DICT:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
elif second_key not in KIDS_G2P_DICT[sam_id]:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
- else:
- print "ERROR: should not be here: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
+ else: # sanity check
+ print "ERROR: first time var already seen?: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
raise SystemExit
- elif OBS_state not in CHECK_DICT[check_key].keys():
+ elif OBS_state not in CHECK_DICT[check_key].keys(): # first time we see this var in this sample with this OBS_state
CHECK_DICT[check_key][OBS_state] = 1
if sam_id not in KIDS_G2P_DICT:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
elif second_key not in KIDS_G2P_DICT[sam_id]:
KIDS_G2P_DICT[sam_id][second_key] = (GT,gene_name,transcript)
+ elif KIDS_G2P_DICT[sam_id][second_key] == (GT,gene_name,transcript): # diff OBS_state, but must have same (GT,gene_name,transcript)
+ pass
else:
- print "ERROR: should not be here: variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
+ print "ERROR: diff (GT,gene_name,transcript) for variant %s in %s gene for CHILD = %s" % (second_key,gene_name,sam_id)
raise SystemExit
- else: # same individual, same variant, same OBS_state
+ else: # same individual, same variant, known OBS_state
# due to the new output of G2P we may have the same variant but with different gene names - ensembl/refseq
# check the gene name in KIDS_G2P_DICT[sam_id][second_key]
if not KIDS_G2P_DICT[sam_id][second_key][1].startswith('ENSG'): # recorded is refseq
--
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