Vcf cnv

VariantValidator/modules/format_converters.py

@@ -164,13 +164,26 @@ def vcf2hgvs_stage1(variant, validator):
     if len(vcf_data) < 4:
         logger.debug("Completed VCF-HVGS step 1 for %s", variant.quibble)
         return False
+
+    # VCF CNV descriptions can be directly converted to a HGVS like description
+    if (re.search("\d+", vcf_data[2]) and (
+            re.search("del", vcf_data[3], re.IGNORECASE) or
+            re.search("inv", vcf_data[3], re.IGNORECASE))):
+
+        if not re.search(r"[gatcnmo]\.", str(vcf_data)):
+            logger.info(f"CNV format identified in {variant.quibble}")
+            cnv_var = f"{vcf_data[0]}:{vcf_data[1]}_{vcf_data[2]}{vcf_data[3].lower()}"
+            logger.info(f"CNV identified, and mapped to {cnv_var}")
+            variant.warnings.append(f"VcfConversionWarning: CNV identified, and mapped to {cnv_var}")
+            variant.quibble = cnv_var
+
     poss_genome = vcf_data[0].lower()
     if ('grch3' in poss_genome or 'hg' in poss_genome) and poss_genome[-1].isdigit():
         vcf_data = vcf_data[1:]
         variant.quibble = '-'.join(vcf_data)
         # TODO test assembly given against settings
         if len(vcf_data) < 4:
-            variant.warnings.append("Insufficient or incorrect  VCF elements provided. "
+            variant.warnings.append("Insufficient or incorrect VCF elements provided. "
                                     "Elements required are chr-pos-ref-alt")
             return True
     # no coordinate found

VariantValidator/modules/vcf_to_pvcf.py

@@ -0,0 +1,129 @@
+class VcfConversionError(Exception):
+    """Custom exception raised when a VCF line cannot be converted to shorthand."""
+    pass
+
+
+def split_vcf_line(vcf_line):
+    """
+    Split a VCF line by detecting delimiter (tab or comma).
+    Raises VcfConversionError if no supported delimiter is found.
+    """
+    line = vcf_line.strip()
+
+    if "\t" in line:
+        return line.split("\t")
+
+    if "," in line:
+        return [f.strip() for f in line.split(",")]
+
+    raise VcfConversionError(
+        "Unable to detect delimiter. Expected tab ('\\t') or comma-separated values."
+    )
+
+
+def vcf_to_shorthand(vcf_line):
+    """
+    Convert a single VCF line into chr-start-end-TYPE shorthand.
+
+    Handles:
+      - CNVs with <DEL>/<DUP>/<INV>
+      - Simple SNVs/indels (chr-pos-ref-alt)
+      - Optional CN field
+
+    Raises:
+      VcfConversionError with descriptive message if conversion fails.
+    """
+
+    # Skip headers
+    if vcf_line.startswith("#"):
+        raise VcfConversionError(
+            "Header line cannot be converted. Please provide a variant record line."
+        )
+
+    fields = split_vcf_line(vcf_line)
+
+    if len(fields) < 5:
+        raise VcfConversionError(
+            f"VCF line has insufficient columns (found {len(fields)}, expected ≥5). "
+            "Ensure the line contains at least CHROM, POS, ID, REF, ALT."
+        )
+
+    chrom, pos, _id, ref, alt = fields[:5]
+    info = fields[7] if len(fields) > 7 else ""
+
+    # Validate position
+    try:
+        pos = int(pos)
+    except ValueError:
+        raise VcfConversionError(
+            f"Invalid POS field: '{pos}' is not an integer."
+        )
+
+    # Structural variants
+    if alt in ("<DEL>", "<DUP>", "<INV>", "DEL", "DUP", "INV"):
+        end = None
+        cn = None
+
+        for entry in info.split(";"):
+            if entry.startswith("END="):
+                try:
+                    end = int(entry.split("=")[1])
+                except ValueError:
+                    raise VcfConversionError(
+                        f"Invalid END value in INFO field: '{entry}'."
+                    )
+
+            elif entry.startswith("SVLEN=") and end is None:
+                try:
+                    end = pos + abs(int(entry.split("=")[1]))
+                except ValueError:
+                    raise VcfConversionError(
+                        f"Invalid SVLEN value in INFO field: '{entry}'."
+                    )
+
+            elif entry.startswith("CN="):
+                cn = entry.split("=")[1]
+
+        if end is None:
+            raise VcfConversionError(
+                "Cannot determine end position for structural variant. "
+                "INFO field must contain END= or SVLEN=."
+            )
+
+        # Remove angle brackets
+        if ">" in alt:
+            alt_clean = alt[1:-1]
+        else:
+            alt_clean = alt
+
+        shorthand = f"{chrom}-{pos}-{end}-{alt_clean}"
+
+        if cn:
+            shorthand += f"[CN{cn}]"
+
+        return shorthand
+
+    # Simple SNV/indel
+    if not ref or not alt:
+        raise VcfConversionError(
+            "Missing REF or ALT allele. Cannot convert variant."
+        )
+
+    return f"{chrom}-{pos}-{ref}-{alt}"
+
+# <LICENSE>
+# Copyright (C) 2016-2026 VariantValidator Contributors
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# </LICENSE>

VariantValidator/modules/vvMixinCore.py

@@ -24,6 +24,7 @@
 from VariantValidator.modules import gene2transcripts
 from VariantValidator.modules import lovd_api
 from VariantValidator.modules import initial_formatting
+from VariantValidator.modules import vcf_to_pvcf
 from VariantValidator.modules.seq_state_to_expanded_repeat import\
         convert_seq_state_to_expanded_repeat
 from VariantValidator.modules.hgvs_utils import hgvs_delins_parts_to_hgvs_obj,\
@@ -115,8 +116,14 @@ def validate(self,
             # Turn each variant into a dictionary. The dictionary will be compiled during validation
             self.batch_list = []
             for queries in batch_queries:
+                # try:
+                #     queries = vcf_to_pvcf.vcf_to_shorthand(queries)
+                # except vcf_to_pvcf.VcfConversionError as e:
+                #     logger.info(f"Cannot convert {queries} into PVCF format {e}")
+                #     pass
                 if isinstance(queries, int):
                     queries = str(queries)
+                    queries = str(queries)
                 queries = queries.strip()
                 query = Variant(queries)
                 self.batch_list.append(query)
@@ -259,6 +266,16 @@ def validate(self,
                         logger.warning(error)
                         continue
 
+                    # VCF line handling - Note: handling csv brings too many issues, so stick to tabs tsv
+                    if "\t" in my_variant.quibble and not re.search(r"[gcrnmo]\.", my_variant.quibble):
+                        try:
+                            my_variant.quibble = vcf_to_pvcf.vcf_to_shorthand(my_variant.quibble)
+                            my_variant.warnings.append(f"VcfConversionWarning: VCF line identified and converted "
+                                                       f"to {my_variant.quibble}")
+                        except vcf_to_pvcf.VcfConversionError as e:
+                            logger.info(f"Cannot convert {my_variant.quibble} into PVCF format {e}")
+                            continue
+
                     # Remove whitespace and quotes
                     my_variant.remove_whitespace()
                     my_variant.remove_quotes()

tests/test_inputs.py

@@ -31255,6 +31255,13 @@ def polyadenylation_b(self):
         results = self.vv.validate('2:g.46707878_46707879insGCAGCGGGAGCG', 'GRCh37', 'mane_select').format_as_dict(test=True)
         assert 'NM_001145051.2:c.457_458insGGGAGCGGCAGC' in results
 
+    def cnv_del_vcf(self):
+        # Test that it fails for genome mismatch
+        results = self.vv.validate('chr1\t1000000\t.\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;END=1005000', 'GRCh38', 'all').format_as_dict(test=True)
+        assert 'intergenic_variant_1' in results
+        assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch38"][
+                "hgvs_genomic_description"] ==  "NC_000001.11:g.1000000_1005000del"
+
 
 # <LICENSE>
 # Copyright (C) 2016-2026 VariantValidator Contributors

tests/test_variantformatter_inputs.py

@@ -6962,6 +6962,17 @@ def test_issue_744b(self):
               }
             }
 
+    def test_vcf_line_variants_del(self):
+        results = VariantFormatter.simpleVariantFormatter.format('chr1\t1000000\t.\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;END=1005000',
+                                                                 'GRCh38', 'all', None, False, True, testing=True)
+        print(results)
+        assert 'chr1:1000000_1005000del' in results.keys()
+
+    def test_vcf_line_variants_inv(self):
+        results = VariantFormatter.simpleVariantFormatter.format('chr1\t1000000\t.\tN\t<INV>\t.\tPASS\tSVTYPE=INV;END=1005000',
+                                                                 'GRCh38', 'all', None, False, True, testing=True)
+        print(results)
+        assert 'chr1:1000000_1005000inv' in results.keys()
 
 
 # <LICENSE>

tests/test_vcf_line_conversion.py

@@ -0,0 +1,121 @@
+import pytest
+
+from VariantValidator.modules import vcf_to_pvcf
+from VariantValidator.modules.vcf_to_pvcf import VcfConversionError
+
+
+# ============================================================
+# Simple SNVs
+# ============================================================
+
+def test_snv_tab_delimited():
+    line = "chr2\t1500000\t.\tA\tT\t.\tPASS\t."
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr2-1500000-A-T"
+
+
+def test_snv_comma_delimited():
+    line = "chr2,1500000,.,G,C,.,PASS,."
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr2-1500000-G-C"
+
+
+# ============================================================
+# Sequence-based indels (standard VCF representation)
+# ============================================================
+
+def test_sequence_deletion():
+    # deletion of "T" at position 1500001
+    line = "chr3\t1500000\t.\tAT\tA\t.\tPASS\t."
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr3-1500000-AT-A"
+
+
+def test_sequence_insertion():
+    # insertion of "T" after A
+    line = "chr3\t1500000\t.\tA\tAT\t.\tPASS\t."
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr3-1500000-A-AT"
+
+
+def test_larger_sequence_deletion():
+    line = "chr5\t2000000\t.\tATGC\tA\t.\tPASS\t."
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr5-2000000-ATGC-A"
+
+
+# ============================================================
+# Symbolic structural variants
+# ============================================================
+
+def test_symbolic_del_with_end():
+    line = "chr1\t1000000\t.\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;END=1005000"
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr1-1000000-1005000-DEL"
+
+
+def test_symbolic_dup_with_svlen():
+    line = "chr1\t2000000\t.\tN\t<DUP>\t.\tPASS\tSVTYPE=DUP;SVLEN=10000"
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr1-2000000-2010000-DUP"
+
+
+def test_symbolic_inv_with_end():
+    line = "chr1\t3000000\t.\tN\t<INV>\t.\tPASS\tSVTYPE=INV;END=3005000"
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr1-3000000-3005000-INV"
+
+
+def test_symbolic_dup_with_copy_number():
+    line = "chr1\t2000000\t.\tN\t<DUP>\t.\tPASS\tSVTYPE=DUP;SVLEN=10000;CN=4"
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr1-2000000-2010000-DUP[CN4]"
+
+
+# ============================================================
+# Comma-separated structural variant
+# ============================================================
+
+def test_comma_separated_structural_variant():
+    line = "chr4,4000000,.,N,<DEL>,.,PASS,SVTYPE=DEL;END=4005000"
+    assert vcf_to_pvcf.vcf_to_shorthand(line) == "chr4-4000000-4005000-DEL"
+
+
+# ============================================================
+# Error handling
+# ============================================================
+
+def test_header_line_raises():
+    with pytest.raises(VcfConversionError):
+        vcf_to_pvcf.vcf_to_shorthand("#CHROM\tPOS\tID\tREF\tALT")
+
+
+def test_insufficient_columns():
+    with pytest.raises(VcfConversionError):
+        vcf_to_pvcf.vcf_to_shorthand("chr1\t100")
+
+
+def test_invalid_pos():
+    with pytest.raises(VcfConversionError):
+        vcf_to_pvcf.vcf_to_shorthand("chr1\tNotAnInt\t.\tA\tT\t.\tPASS\t.")
+
+
+def test_missing_end_for_symbolic_sv():
+    with pytest.raises(VcfConversionError):
+        vcf_to_pvcf.vcf_to_shorthand("chr1\t1000000\t.\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL")
+
+
+def test_unknown_delimiter():
+    with pytest.raises(VcfConversionError):
+        vcf_to_pvcf.vcf_to_shorthand("chr1|1000000|.|A|T")
+
+
+# <LICENSE>
+# Copyright (C) 2016-2026 VariantValidator Contributors
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# </LICENSE>
+
+