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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
scout/__version__.py CHANGED
@@ -1 +1 @@
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- __version__ = "4.89.1"
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+ __version__ = "4.89.2"
@@ -335,7 +335,7 @@ class GeneHandler(object):
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  Returns:
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  alias_genes(dict): {<hgnc_alias>: {'true': <hgnc_id>, 'ids': {<hgnc_id_1>, <hgnc_id_2>, ...}}}
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  """
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- LOG.debug("Fetching all genes by alias")
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+
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  # Collect one entry for each alias symbol that exists
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  alias_genes = {}
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scout/parse/panel.py CHANGED
@@ -2,7 +2,7 @@
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  import logging
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  from datetime import datetime
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- from typing import Dict, List, Optional
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+ from typing import Dict, Optional
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  from scout.constants import (
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  INCOMPLETE_PENETRANCE_MAP,
@@ -383,7 +383,7 @@ def parse_panel_app_panel(
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  return gene_panel
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- def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
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+ def get_omim_panel_genes(genemap2_lines: list, mim2gene_lines: list, alias_genes: dict):
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  """Return all genes that should be included in the OMIM-AUTO panel
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  Return the hgnc symbols
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@@ -424,6 +424,19 @@ def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
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  break
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  if hgnc_id_info:
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- yield {"hgnc_id": hgnc_id_info["true"], "hgnc_symbol": hgnc_symbol}
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+ if hgnc_id_info["true"]:
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+ hgnc_id = hgnc_id_info["true"]
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+ elif len(hgnc_id_info.get("ids", ())) == 1:
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+ hgnc_id = list(hgnc_id_info["ids"])[0]
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+ LOG.warning(
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+ "Gene symbol %s does not exist: using an apparently unique alias for hgnc_id %s",
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+ hgnc_symbol,
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+ hgnc_id,
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+ )
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+ else:
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+ LOG.warning(
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+ "Gene symbol %s does not exist, and as an alias it is not unique", hgnc_symbol
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+ )
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+ yield {"hgnc_id": hgnc_id, "hgnc_symbol": hgnc_symbol}
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  else:
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  LOG.warning("Gene symbol %s does not exist", hgnc_symbol)
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: scout-browser
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- Version: 4.89.1
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+ Version: 4.89.2
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  Summary: Clinical DNA variant visualizer and browser.
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  Home-page: https://github.com/Clinical-Genomics/scout
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  Author: Måns Magnusson
@@ -1,5 +1,5 @@
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  scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
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- scout/__version__.py,sha256=3KeIGQ1or1A7hNSvFFP7OkoHzZ6E8eZ1A06st7yz9DM,23
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+ scout/__version__.py,sha256=T7ThRIRkePjiRTDa6aeTTkyfBdSPI1nLqcsHeWWi8Ig,23
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  scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
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  scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
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  scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -13,7 +13,7 @@ scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7
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  scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
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  scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
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  scout/adapter/mongo/filter.py,sha256=vzBJS_6vq2z76SH8PszdRR-MNuZ7_RA4VJvnkNYUs7s,8937
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- scout/adapter/mongo/hgnc.py,sha256=9jbrkaTtlnnuE5gsSM8ylb8Kero4lC2zCWr-90QlyAY,16420
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+ scout/adapter/mongo/hgnc.py,sha256=FUzzj9at62jW-ypII6mWrfeDTdQzW4BWgXg3bWRTqGo,16372
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  scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
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  scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
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  scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -410,7 +410,7 @@ scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,952
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  scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
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  scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
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  scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
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- scout/parse/panel.py,sha256=4HYjokWh2sF-effLQxPf4ZzRHsf9grqF1Z9f-HAaRmk,13153
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+ scout/parse/panel.py,sha256=xNIzUhyCOBIWtH2avbVvJgZioanMztImG6dV1wXnyO4,13722
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  scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
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  scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
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  scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
@@ -672,9 +672,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
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  scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
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  scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
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  scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
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- scout_browser-4.89.1.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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- scout_browser-4.89.1.dist-info/METADATA,sha256=Ox8i_nZ8B2KbERsn_QzPK9jCDsbSPA7IYNjiuH673Pg,14262
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- scout_browser-4.89.1.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
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- scout_browser-4.89.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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- scout_browser-4.89.1.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
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- scout_browser-4.89.1.dist-info/RECORD,,
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+ scout_browser-4.89.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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+ scout_browser-4.89.2.dist-info/METADATA,sha256=stc_17UT_s4jOKJezGHaktPrwY-h3IJqt1VnGQfm6uI,14262
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+ scout_browser-4.89.2.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
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+ scout_browser-4.89.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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+ scout_browser-4.89.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
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+ scout_browser-4.89.2.dist-info/RECORD,,