Build results/figures: genotype and filtered results ignored

build_figures.py

@@ -200,8 +200,11 @@ def build_recall_precision_graphs(tools, output_dir):
 def init(input_dir, nb_inds, haploid, stripplot, output):
     os.chdir(input_dir)
     tools = ["breakdancer", "delly", "lumpy", "pindel", "cnvnator", "genomestrip", "Filtered_results"]
-    build_genotype_quality_graphs(tools, nb_inds, haploid, stripplot, output)
     build_recall_precision_graphs(tools, output)
+    if len(glob.glob("*sv_genotypes_quality_per_tools.tsv")) > 0:
+        build_genotype_quality_graphs(tools, nb_inds, haploid, stripplot, output)
+    else:
+        print("No genotypes found. Step ignored.")
 
 
 def main():

build_results.py

@@ -813,9 +813,10 @@ def build_body_cells(rec_keys, records, nb_records, nb_inds, tools, cells, cells
         ###############################################################################
         # Until we have filled all tools, check if the record is kept after filtering: #
         ###############################################################################
-        cells, cells_gt, cells_gq = apply_style_of_filter_cells(cells, cells_gt, cells_gq, i, is_kept, nb_records,
-                                                                nb_inds, nb_tools, filtered_records, do_genotype,
-                                                                rec_id)
+        if filtered_records is not None:
+            cells, cells_gt, cells_gq = apply_style_of_filter_cells(cells, cells_gt, cells_gq, i, is_kept, nb_records,
+                                                                    nb_inds, nb_tools, filtered_records, do_genotype,
+                                                                    rec_id)
 
         i += 1
 
@@ -858,9 +859,10 @@ def init(output, vcf_folder, true_vcf, filtered_vcfs=None, genotypes_files=None,
     eprint(" Reading file %s" % true_ones)
     sv_set_to, true_ones_records = read_vcf_file(true_ones)
     sv_set += sv_set_to
-    filtered_records = []
+    filtered_records = None
 
     if filtered_vcfs:
+        filtered_records = []
         for filtered_vcf in filtered_vcfs:
             eprint(" Reading file %s" % filtered_vcf)
             filtered_records += read_vcf_file(filtered_vcf)[1]