From 86c8c0be5d133482667fe270363ad805c0ecfa12 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Thu, 2 Nov 2017 15:03:37 +0100
Subject: [PATCH] Fix inversions: reverse complement
---
build_pop.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/build_pop.py b/build_pop.py
index 520f5de..8cb345c 100755
--- a/build_pop.py
+++ b/build_pop.py
@@ -9,6 +9,7 @@ import traceback
from collections import OrderedDict
import vcf
from Bio import SeqIO
+from Bio.Seq import Seq
import tempfile
from pysam import tabix_compress, tabix_index, VariantFile
from variants_simulator import VariantsSimulator
@@ -371,7 +372,8 @@ def _build_fastas_inversions(fasta_orig_chrm: dict, genotypes_for_inds: dict, nb
if genotype[k] == "1":
start = int(props["start"])
end = int(props["end"])
- fastas[i][k] = fastas[i][k][:start] + fastas[i][k][start:end][::-1] + fastas[i][k][end:]
+ fastas[i][k] = fastas[i][k][:start] + str(Seq(fastas[i][k][start:end]).reverse_complement()) + \
+ fastas[i][k][end:]
i += 1
return fastas
--
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