Ad type of variant to build_results script

build_results.py

@@ -38,6 +38,8 @@ COLOR_IS_KEPT = "#81F781"
 COLOR_FALSE_POSITIVE = "#FE642E"
 COLOR_WRONG_GT = "#B40404"
 
+ALLOW_VARIANTS = ['del', 'inv']
+
 
 def get_args():
     """
@@ -51,6 +53,7 @@ description: Build results of the simulated data detection")
     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='File listing VCF files containing the filtered results')
+    parser.add_argument('-t', '--type', type="str", choices=ALLOW_VARIANTS, help="Type of variant")
     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')
@@ -86,19 +89,23 @@ def passed_variant(record):
     return record.filter is None or len(record.filter) == 0 or "PASS" in record.filter
 
 
-def read_vcf_file(infile):
+def read_vcf_file(infile, type_v):
     """
     Read a vcf file
     :param infile: vcf file path
+    :param type_v: type of variant ("del" or "inv")
     :return: set or records, list of records ids
     """
+    if type_v.lower() not in ALLOW_VARIANTS:
+        raise ValueError("Invalid variant type: %s" % type_v)
     SVSet=[]
     ids = []
     for record in VCFReader(infile):
-        if not passed_variant(record):
-            continue
-        SVSet.append(record)
-        ids.append(record.id)
+        if record.sv_type.lower() == type_v:
+            if not passed_variant(record):
+                continue
+            SVSet.append(record)
+            ids.append(record.id)
     return SVSet, ids
 
     
@@ -811,8 +818,9 @@ def build_xlsx_cols():
             XLSX_COLS.append(alp + j)
 
 
-def init(output, vcf_files, true_vcf, filtered_vcfs=None, overlap_cutoff=0.5,
+def init(output, vcf_files, true_vcf, filtered_vcfs=None, type_v="del", overlap_cutoff=0.5,
          left_precision=sys.maxsize, right_precision=sys.maxsize, no_xls=False, haploid=False):
+
     build_xlsx_cols()
 
     genotypes = {}
@@ -837,12 +845,12 @@ def init(output, vcf_files, true_vcf, filtered_vcfs=None, overlap_cutoff=0.5,
     for infile in vcf_files:
         eprint(" Reading file %s" % infile)
         try:
-            sv_set += read_vcf_file(infile)[0]
+            sv_set += read_vcf_file(infile, type_v)[0]
         except:
             print("Ignoreing file %s" % infile)
 
     eprint(" Reading file %s" % true_vcf)
-    sv_set_to, true_ones_records = read_vcf_file(true_vcf)
+    sv_set_to, true_ones_records = read_vcf_file(true_vcf, type_v)
     sv_set += sv_set_to
 
     # Compute connected components:
@@ -924,8 +932,16 @@ def main():
     """
     # parse the command line args
     args = get_args()
-    init(args.output, get_vcf_files(args.vcfs), args.true_vcf, get_vcf_files(args.filtered_vcf), args.overlap_cutoff,
-         args.left_precision, args.right_precision, args.no_xls, args.haploid)
+    init(output=args.output,
+         vcf_files=get_vcf_files(args.vcfs),
+         true_vcf=args.true_vcf,
+         filtered_vcfs=get_vcf_files(args.filtered_vcf),
+         type_v=args.type,
+         overlap_cutoff=args.overlap_cutoff,
+         left_precision=args.left_precision,
+         right_precision=args.right_precision,
+         no_xls=args.no_xls,
+         haploid=args.haploid)
 
 
 # initialize the script

lib @ 280518a4

-Subproject commit 3cc040bf648e76d911ef7f65ccef78a6ad8695f4
+Subproject commit 280518a443d37a579762928940355aafb571b671