scout-browser 4.89.1__py3-none-any.whl → 4.89.2__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.89.1"
+__version__ = "4.89.2"

scout/adapter/mongo/hgnc.py

@@ -335,7 +335,7 @@ class GeneHandler(object):
         Returns:
             alias_genes(dict): {<hgnc_alias>: {'true': <hgnc_id>, 'ids': {<hgnc_id_1>, <hgnc_id_2>, ...}}}
         """
-        LOG.debug("Fetching all genes by alias")
+
         # Collect one entry for each alias symbol that exists
         alias_genes = {}
 

scout/parse/panel.py

@@ -2,7 +2,7 @@
 
 import logging
 from datetime import datetime
-from typing import Dict, List, Optional
+from typing import Dict, Optional
 
 from scout.constants import (
     INCOMPLETE_PENETRANCE_MAP,
@@ -383,7 +383,7 @@ def parse_panel_app_panel(
     return gene_panel
 
 
-def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
+def get_omim_panel_genes(genemap2_lines: list, mim2gene_lines: list, alias_genes: dict):
     """Return all genes that should be included in the OMIM-AUTO panel
     Return the hgnc symbols
 
@@ -424,6 +424,19 @@ def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
                 break
 
         if hgnc_id_info:
-            yield {"hgnc_id": hgnc_id_info["true"], "hgnc_symbol": hgnc_symbol}
+            if hgnc_id_info["true"]:
+                hgnc_id = hgnc_id_info["true"]
+            elif len(hgnc_id_info.get("ids", ())) == 1:
+                hgnc_id = list(hgnc_id_info["ids"])[0]
+                LOG.warning(
+                    "Gene symbol %s does not exist: using an apparently unique alias for hgnc_id %s",
+                    hgnc_symbol,
+                    hgnc_id,
+                )
+            else:
+                LOG.warning(
+                    "Gene symbol %s does not exist, and as an alias it is not unique", hgnc_symbol
+                )
+            yield {"hgnc_id": hgnc_id, "hgnc_symbol": hgnc_symbol}
         else:
             LOG.warning("Gene symbol %s does not exist", hgnc_symbol)

{scout_browser-4.89.1.dist-info → scout_browser-4.89.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.89.1
+Version: 4.89.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout_browser-4.89.1.dist-info → scout_browser-4.89.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=3KeIGQ1or1A7hNSvFFP7OkoHzZ6E8eZ1A06st7yz9DM,23
+scout/__version__.py,sha256=T7ThRIRkePjiRTDa6aeTTkyfBdSPI1nLqcsHeWWi8Ig,23
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -13,7 +13,7 @@ scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7
 scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
 scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
 scout/adapter/mongo/filter.py,sha256=vzBJS_6vq2z76SH8PszdRR-MNuZ7_RA4VJvnkNYUs7s,8937
-scout/adapter/mongo/hgnc.py,sha256=9jbrkaTtlnnuE5gsSM8ylb8Kero4lC2zCWr-90QlyAY,16420
+scout/adapter/mongo/hgnc.py,sha256=FUzzj9at62jW-ypII6mWrfeDTdQzW4BWgXg3bWRTqGo,16372
 scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
 scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
 scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -410,7 +410,7 @@ scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,952
 scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
 scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
 scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
-scout/parse/panel.py,sha256=4HYjokWh2sF-effLQxPf4ZzRHsf9grqF1Z9f-HAaRmk,13153
+scout/parse/panel.py,sha256=xNIzUhyCOBIWtH2avbVvJgZioanMztImG6dV1wXnyO4,13722
 scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
 scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
 scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
@@ -672,9 +672,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.89.1.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.89.1.dist-info/METADATA,sha256=Ox8i_nZ8B2KbERsn_QzPK9jCDsbSPA7IYNjiuH673Pg,14262
-scout_browser-4.89.1.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-scout_browser-4.89.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.89.1.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.89.1.dist-info/RECORD,,
+scout_browser-4.89.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.89.2.dist-info/METADATA,sha256=stc_17UT_s4jOKJezGHaktPrwY-h3IJqt1VnGQfm6uI,14262
+scout_browser-4.89.2.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+scout_browser-4.89.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.89.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.89.2.dist-info/RECORD,,