Replace vawk by python code

build_results.py

@@ -196,22 +196,19 @@ def get_genotypes(genotypes_file, true_vcf_file):
     """
     genotypes = {}
     gt_quality = {}
-    nb_inds = 0
-    # Genotypes:
-    genotypes_raw = os.popen("zcat " + genotypes_file + " " + true_vcf_file + " | " +
-                             os.path.join(prg_path, "vawk") + " '{ print $3,S$*$GT}'").read().split("\n")
-    for gt in genotypes_raw:
-        if gt != "":
-            gt_l = gt.split("\t")
-            genotypes[gt_l[0]] = gt_l[1:]
-            nb_inds = len(gt_l[1:])
-
-    gt_quality_raw = os.popen("zcat " + genotypes_file + " | " +
-                              os.path.join(prg_path, "vawk") + " '{ print $3,S$*$GQ}'").read().split("\n")
-    for gq in gt_quality_raw:
-        if gq != "":
-            gq_l = gq.split("\t")
-            gt_quality[gq_l[0]] = gq_l[1:]
+
+    # Real data:
+    reader_t = vcf.VCFReader(filename=true_vcf_file)
+    for rec_t in reader_t:
+        genotypes[rec_t.ID] = [x.data.GT for x in rec_t.samples]
+
+    nb_inds = len(list(genotypes.values())[0])
+
+    # Samples:
+    reader = vcf.VCFReader(filename=genotypes_file)
+    for rec in reader:
+        genotypes[rec.ID] = [x.data.GT for x in rec.samples]
+        gt_quality[rec.ID] = [x.data.GQ for x in rec.samples]
 
     return genotypes, gt_quality, nb_inds
 
@@ -738,7 +735,7 @@ def main():
                     if args.genotypes:
                         # Genotype (sheets 2&3):
                         cells_gt, cells_gq = fill_genotypes_data(i, 2 + ((nb_tools + 1) * nb_inds), cells_gt, cells_gq,
-                                                             record["tools"][tool], my_genotypes, args.haploid)
+                                                                 record["tools"][tool], my_genotypes, args.haploid)
                 else:
                     sv_format = {}