@@ -84,7 +84,10 @@ def get_ipr_statements_from_variants(
84
84
]
85
85
86
86
for ipr_row in convert_statements_to_alterations (
87
- graphkb_conn , inferred_statements , disease_name , convert_to_rid_set (inferred_matches )
87
+ graphkb_conn ,
88
+ inferred_statements ,
89
+ disease_name ,
90
+ convert_to_rid_set (inferred_matches ),
88
91
):
89
92
ipr_row ["kbData" ]["inferred" ] = True
90
93
rows .append (ipr_row )
@@ -122,16 +125,16 @@ def annotate_expression_variants(
122
125
continue
123
126
try :
124
127
matches = gkb_match .match_expression_variant (graphkb_conn , gene , variant )
125
- for matched_stmt in get_ipr_statements_from_variants (graphkb_conn , matches , disease_name ):
128
+ for matched_stmt in get_ipr_statements_from_variants (
129
+ graphkb_conn , matches , disease_name
130
+ ):
126
131
ipr_row = {
127
- ' variant' : row [' key' ],
128
- ' variantType' : row .get (' variantType' , ' exp' ),
129
- ' kbVariantId' : matched_stmt [' kbVariantId' ],
130
- ' kbVariant' : matched_stmt [' kbVariant' ],
131
- ' kbMatchedStatements' : [matched_stmt ]
132
+ " variant" : row [" key" ],
133
+ " variantType" : row .get (" variantType" , " exp" ),
134
+ " kbVariantId" : matched_stmt [" kbVariantId" ],
135
+ " kbVariant" : matched_stmt [" kbVariant" ],
136
+ " kbMatchedStatements" : [matched_stmt ],
132
137
}
133
- #ipr_row["variant"] = row["key"]
134
- #ipr_row["variantType"] = row.get("variantType", "exp")
135
138
alterations .append (ipr_row )
136
139
except FeatureNotFoundError as err :
137
140
problem_genes .add (gene )
@@ -182,21 +185,17 @@ def annotate_copy_variants(
182
185
continue
183
186
try :
184
187
matches = gkb_match .match_copy_variant (graphkb_conn , gene , variant )
185
- #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
186
- # ipr_row["variant"] = row["key"]
187
- # ipr_row["variantType"] = row.get("variantType", "cnv")
188
- # alterations.append(ipr_row)
189
- for matched_stmt in get_ipr_statements_from_variants (graphkb_conn , matches , disease_name ):
188
+ for matched_stmt in get_ipr_statements_from_variants (
189
+ graphkb_conn , matches , disease_name
190
+ ):
190
191
ipr_row = {
191
- ' variant' : row [' key' ],
192
- ' variantType' : row .get (' variantType' , ' cnv' ),
193
- ' kbVariantId' : matched_stmt [' kbVariantId' ],
194
- ' kbVariant' : matched_stmt [' kbVariant' ],
195
- ' kbMatchedStatements' : [matched_stmt ]
192
+ " variant" : row [" key" ],
193
+ " variantType" : row .get (" variantType" , " cnv" ),
194
+ " kbVariantId" : matched_stmt [" kbVariantId" ],
195
+ " kbVariant" : matched_stmt [" kbVariant" ],
196
+ " kbMatchedStatements" : [matched_stmt ],
196
197
}
197
198
alterations .append (ipr_row )
198
- #ipr_row["variant"] = row["key"]
199
- #ipr_row["variantType"] = row.get("variantType", "exp")
200
199
except FeatureNotFoundError as err :
201
200
problem_genes .add (gene )
202
201
logger .debug (f"Unrecognized gene ({ gene } { variant } ): { err } " )
@@ -270,23 +269,17 @@ def annotate_positional_variants(
270
269
matches = gkb_match .match_positional_variant (graphkb_conn , variant )
271
270
else :
272
271
raise parse_err
273
- for matched_stmt in get_ipr_statements_from_variants (graphkb_conn , matches , disease_name ):
272
+ for matched_stmt in get_ipr_statements_from_variants (
273
+ graphkb_conn , matches , disease_name
274
+ ):
274
275
ipr_row = {
275
- ' variant' : row [' key' ],
276
- ' variantType' : row .get ("variantType" , "mut" if row .get ("gene" ) else "sv" ),
277
- ' kbVariant' : matched_stmt [' kbVariant' ],
278
- ' kbVariantId' : matched_stmt [' kbVariantId' ],
279
- ' kbMatchedStatements' : [matched_stmt ]
276
+ " variant" : row [" key" ],
277
+ " variantType" : row .get ("variantType" , "mut" if row .get ("gene" ) else "sv" ),
278
+ " kbVariant" : matched_stmt [" kbVariant" ],
279
+ " kbVariantId" : matched_stmt [" kbVariantId" ],
280
+ " kbMatchedStatements" : [matched_stmt ],
280
281
}
281
282
alterations .append (Hashabledict (ipr_row ))
282
- #for ipr_row in get_ipr_statements_from_variants(
283
- # graphkb_conn, matches, disease_name
284
- #):
285
- # ipr_row["variant"] = row["key"]
286
- # ipr_row["variantType"] = row.get(
287
- # "variantType", "mut" if row.get("gene") else "sv"
288
- # )
289
- # alterations.append(Hashabledict(ipr_row))
290
283
291
284
except FeatureNotFoundError as err :
292
285
logger .debug (f"failed to match positional variants ({ variant } ): { err } " )
@@ -344,7 +337,10 @@ def annotate_msi(
344
337
"target" : {
345
338
"target" : "CategoryVariant" ,
346
339
"filters" : {
347
- "reference1" : {"target" : "Signature" , "filters" : {"name" : msi_category }}
340
+ "reference1" : {
341
+ "target" : "Signature" ,
342
+ "filters" : {"name" : msi_category },
343
+ }
348
344
},
349
345
},
350
346
"queryType" : "similarTo" ,
@@ -353,24 +349,24 @@ def annotate_msi(
353
349
)
354
350
if msi_categories :
355
351
msi_variants = [cast (Variant , var ) for var in msi_categories ]
356
- for matched_stmt in get_ipr_statements_from_variants (graphkb_conn , msi_variants , disease_name ):
352
+ for matched_stmt in get_ipr_statements_from_variants (
353
+ graphkb_conn , msi_variants , disease_name
354
+ ):
357
355
ipr_row = {
358
- ' variant' : msi_category ,
359
- ' variantType' : ' msi' ,
360
- ' kbVariantId' : matched_stmt [' kbVariantId' ],
361
- ' kbVariant' : matched_stmt [' kbVariant' ],
362
- ' kbMatchedStatements' : [matched_stmt ]
356
+ " variant" : msi_category ,
357
+ " variantType" : " msi" ,
358
+ " kbVariantId" : matched_stmt [" kbVariantId" ],
359
+ " kbVariant" : matched_stmt [" kbVariant" ],
360
+ " kbMatchedStatements" : [matched_stmt ],
363
361
}
364
362
gkb_matches .append (ipr_row )
365
- #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, msi_variants, disease_name):
366
- # ipr_row["variant"] = msi_category
367
- # ipr_row["variantType"] = "msi"
368
- # gkb_matches.append(ipr_row)
369
363
return gkb_matches
370
364
371
365
372
366
def annotate_tmb (
373
- graphkb_conn : GraphKBConnection , disease_name : str = "cancer" , category : str = TMB_HIGH_CATEGORY
367
+ graphkb_conn : GraphKBConnection ,
368
+ disease_name : str = "cancer" ,
369
+ category : str = TMB_HIGH_CATEGORY ,
374
370
) -> List [KbMatch ]:
375
371
"""Annotate Tumour Mutation Burden (tmb) categories from GraphKB in the IPR alterations format.
376
372
@@ -401,17 +397,15 @@ def annotate_tmb(
401
397
)
402
398
if categories :
403
399
cat_variants = [cast (Variant , var ) for var in categories ]
404
- for matched_stmt in get_ipr_statements_from_variants (graphkb_conn , cat_variants , disease_name ):
400
+ for matched_stmt in get_ipr_statements_from_variants (
401
+ graphkb_conn , cat_variants , disease_name
402
+ ):
405
403
ipr_row = {
406
- ' variant' : category ,
407
- ' variantType' : ' tmb' ,
408
- ' kbVariantId' : matched_stmt [' kbVariantId' ],
409
- ' kbVariant' : matched_stmt [' kbVariant' ],
410
- ' kbMatchedStatements' : [matched_stmt ]
404
+ " variant" : category ,
405
+ " variantType" : " tmb" ,
406
+ " kbVariantId" : matched_stmt [" kbVariantId" ],
407
+ " kbVariant" : matched_stmt [" kbVariant" ],
408
+ " kbMatchedStatements" : [matched_stmt ],
411
409
}
412
410
gkb_matches .append (ipr_row )
413
- #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, cat_variants, disease_name):
414
- # ipr_row["variant"] = category
415
- # ipr_row["variantType"] = "tmb"
416
- # gkb_matches.append(ipr_row)
417
411
return gkb_matches
0 commit comments