Fix inversions: reverse complement

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