Make build_results working with the new snk pipeline

build_results.py

@@ -47,11 +47,10 @@ def get_args():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter, description="\
 Build Results \n \
 description: Build results of the simulated data detection")
-    parser.add_argument('-v', '--vcf', type=str, required=True, help='folder containing all vcf results files')
+    parser.add_argument('-v', '--vcfs', type=str, required=True, help='Vcf files for each detection tool', nargs='+')
     parser.add_argument('-t', '--true-vcf', type=str, required=True, help='VCF file containing the simulated deletions')
     parser.add_argument('-f', '--filtered-vcf', type=str, required=False,
                         help='VCF file containing the filtered results', nargs='+')
-    parser.add_argument('-g', '--genotypes', type=str, help="VCF file containing genotypes", nargs='+')
     parser.add_argument('--overlap_cutoff',  type=float, default=0.5, help='cutoff for reciprocal overlap')
     parser.add_argument('--left_precision',  type=int, default=-1, help='left breakpoint precision')
     parser.add_argument('--right_precision',  type=int, default=-1, help='right breakpoint precision')
@@ -611,23 +610,6 @@ def create_tsv_file(filename: str, headers: list, cells: dict, nb_tools: int, nb
         tsv_file.write(tsv)
 
 
-def search_vcf_files(my_folder):
-    """
-    Search vcf files recursively (can be replaced by glob, but required python >= 3.5
-    (3.4 version in genotoul plateform)
-    :param my_folder: folder into search files
-    :return: list of vcf files, with absolute paths
-    """
-    vcf_files = []
-    for item in os.listdir(my_folder):
-        item_file = os.path.join(my_folder, item)
-        if os.path.isfile(item_file) and (item_file.endswith(".vcf") or item_file.endswith(".vcf.gz")):
-            vcf_files.append(os.path.abspath(item_file))
-        elif os.path.isdir(item_file):
-            vcf_files += search_vcf_files(item_file)
-    return vcf_files
-
-
 def print_results(nb_records, orphans, with_xlsx, output, do_genotype):
     """
     Print list of outputs
@@ -829,7 +811,7 @@ def build_xlsx_cols():
             XLSX_COLS.append(alp + j)
 
 
-def init(output, vcf_folder, true_vcf, filtered_vcfs=None, genotypes_files=None, overlap_cutoff=0.5,
+def init(output, vcf_files, true_vcf, filtered_vcfs=None, overlap_cutoff=0.5,
          left_precision=sys.maxsize, right_precision=sys.maxsize, no_xls=False, haploid=False):
     build_xlsx_cols()
 
@@ -838,34 +820,30 @@ def init(output, vcf_folder, true_vcf, filtered_vcfs=None, genotypes_files=None,
 
     nb_inds = 0
 
-    if genotypes_files:
-        genotypes, gt_quality, nb_inds = get_genotypes(genotypes_files, true_vcf)
-
-    do_genotype = genotypes_files is not None
+    filtered_records = None
+    do_genotype = False
 
-    filenames = search_vcf_files(vcf_folder)
+    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]
 
-    true_ones = true_vcf
+        genotypes, gt_quality, nb_inds = get_genotypes(filtered_vcfs, true_vcf)
+        do_genotype = True
 
     # Reading all the vcf files
     sv_set = []
-    for infile in filenames:
+    for infile in vcf_files:
         eprint(" Reading file %s" % infile)
         try:
             sv_set += read_vcf_file(infile)[0]
         except:
             print("Ignoreing file %s" % infile)
 
-    eprint(" Reading file %s" % true_ones)
-    sv_set_to, true_ones_records = read_vcf_file(true_ones)
+    eprint(" Reading file %s" % true_vcf)
+    sv_set_to, true_ones_records = read_vcf_file(true_vcf)
     sv_set += sv_set_to
-    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]
 
     # Compute connected components:
     eprint("Computing Connected components")
@@ -931,7 +909,7 @@ def main():
     """
     # parse the command line args
     args = get_args()
-    init(args.output, args.vcf, args.true_vcf, args.filtered_vcf, args.genotypes, args.overlap_cutoff,
+    init(args.output, args.vcfs, args.true_vcf, args.filtered_vcf, args.overlap_cutoff,
          args.left_precision, args.right_precision, args.no_xls, args.haploid)