Merge branch 'master' into SP-3283-improve-the-python-api-client-to-i…

…nclude-more-cases
saphetor · Aug 11, 2022 · 908275b · 908275b
2 parents 9b882b1 + 62fe591
commit 908275b
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Showing 3 changed files with 12 additions and 2 deletions.
diff --git a/README.md b/README.md
@@ -258,6 +258,8 @@ To annotate the VCF file with the annotations that you are interested in, you ne
 from varsome_api.vcf import VCFAnnotator
 from vcf.parser import _Info, _encode_type
 class MyVCFAnnotator(VCFAnnotator):
+
+
     def annotate_record(self, record, variant_result, original_variant):
         """
         :param record: vcf record object

diff --git a/varsome_api/models/elements/acmg.py b/varsome_api/models/elements/acmg.py
@@ -51,3 +51,6 @@ class ACMG(models.Base):
     verdict = fields.EmbeddedField(
         ACMGVerdict, nullable=True, required=False, help_text="ACMG Verdict"
     )
+    coding_impact = fields.StringField(required=False, nullable=True)
+    transcript = fields.StringField(required=False, nullable=True)
+    transcript_reason = fields.StringField(required=False, nullable=True)
diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py
@@ -227,12 +227,17 @@ def annotate(self, input_vcf_file, output_vcf_file=None, template=None, **kwargs
                     input_batch = OrderedDict()
                     batch_limit = self.max_variants_per_batch * self.max_threads * 2
                     for record in reader:
+                        reference_sequence = record.REF
+                        if reference_sequence is None or reference_sequence == ".":
+                            reference_sequence = ""
                         for alt_seq in record.ALT:
+                            if alt_seq is None or alt_seq == ".":
+                                alt_seq = ""
                             requested_variant = "%s:%s:%s:%s" % (
                                 record.CHROM,
                                 record.POS,
-                                record.REF or "",
-                                alt_seq or "",
+                                reference_sequence,
+                                alt_seq,
                             )
                             input_batch[requested_variant] = record
                             self.total_variants += 1