Merge pull request #113 from bcgsc/improvement/DEVSU-1885_fix_malform…

…ed_deletions

Improvement/devsu 1885 fix malformed deletions

ipr/annotate.py

@@ -331,7 +331,22 @@ def annotate_positional_variants(
             if not variant:
                 continue
             try:
-                matches = gkb_match.match_positional_variant(graphkb_conn, variant)
+                try:
+                    matches = gkb_match.match_positional_variant(graphkb_conn, variant)
+                except HTTPError:
+                    # DEVSU-1885 - fix malformed single deletion described as substitution of blank
+                    # eg.
+                    if (
+                        variant[-1] == '>'
+                        and 'g.' in variant
+                        and variant[-2].isalpha()
+                        and variant[-3].isnumeric()
+                    ):
+                        logger.warning(
+                            f"Assuming malformed deletion variant {variant} is {variant[:-2] + 'del'}"
+                        )
+                        variant = variant[:-2] + 'del'
+                        matches = gkb_match.match_positional_variant(graphkb_conn, variant)
 
                 # GERO-299 - check for conflicting nonsense and missense categories
                 missense = [

ipr/ipr.py

@@ -5,12 +5,11 @@
 from graphkb import GraphKBConnection
 from graphkb import statement as gkb_statement
 from graphkb import vocab as gkb_vocab
-from graphkb.types import Record
 from typing import Dict, Iterable, List, Sequence, Set, Tuple
 
 from .constants import GERMLINE_BASE_TERMS, VARIANT_CLASSES
 from .types import GkbStatement, ImageDefinition, IprFusionVariant, IprGene, IprVariant, KbMatch
-from .util import convert_to_rid_set, find_variant, logger
+from .util import find_variant, logger
 
 
 def display_evidence_levels(statement: GkbStatement) -> str:

setup.cfg

@@ -18,7 +18,7 @@ known_standard_library = requests
 
 [metadata]
 name = ipr
-version = 3.7.1
+version = 3.8.0
 author_email = ipr@bcgsc.ca
 author = ipr
 maintainer_email = ipr@bcgsc.ca