From 2c7499b42640d0396f203cd0d680fa7c404521ec Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Fri, 25 Aug 2017 15:57:49 +0200
Subject: [PATCH] Fix genotypes in build results
---
build_results.py | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/build_results.py b/build_results.py
index af9fb38..dc33194 100755
--- a/build_results.py
+++ b/build_results.py
@@ -174,9 +174,10 @@ def get_genotypes(genotypes_file, true_vcf_file):
# Real data:
reader_t = VariantFile(true_vcf_file)
+ samples_t = None
for rec_t in reader_t:
- samples = rec_t.samples
- genotypes[rec_t.id] = ["/".join(map(str, samples[x]["GT"])) for x in samples]
+ samples_t = rec_t.samples
+ genotypes[rec_t.id] = ["/".join(map(str, samples_t[x]["GT"])) for x in samples_t]
nb_inds = len(list(genotypes.values())[0])
@@ -184,8 +185,9 @@ def get_genotypes(genotypes_file, true_vcf_file):
reader = VariantFile(genotypes_file)
for rec in reader:
samples = rec.samples
- genotypes[rec.id] = ["/".join(map(str, samples[x]["GT"])) for x in samples]
- gt_quality[rec.id] = [samples[x]["GQ"] for x in samples]
+ genotypes[rec.id] = ["/".join(map(str, samples[x]["GT"])) for x in samples_t.keys()] # Fixed: use samples keys
+ # from real data to keep the same order
+ gt_quality[rec.id] = [samples[x]["GQ"] for x in samples_t.keys()]
return genotypes, gt_quality, nb_inds
--
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