pheval-exomiser 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

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Files changed (5) hide show
  1. pheval_exomiser/post_process/post_process_results_format.py +6 -3
  2. {pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/METADATA +4 -4
  3. {pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/RECORD +5 -5
  4. {pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/WHEEL +0 -0
  5. {pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/entry_points.txt +0 -0
pheval_exomiser/post_process/post_process_results_format.py CHANGED
@@ -35,11 +35,12 @@ def trim_exomiser_result_filename(exomiser_result_path: Path) -> Path:
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  def extract_gene_results_from_json(
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  exomiser_json_result: pl.DataFrame, score_name: str
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  ) -> pl.DataFrame:
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+ score_expr = pl.col(score_name) if score_name in exomiser_json_result.columns else pl.lit(0.0)
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  return exomiser_json_result.select(
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  [
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  pl.col("geneSymbol").alias("gene_symbol"),
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  pl.col("geneIdentifier").struct.field("geneId").alias("gene_identifier"),
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- pl.col(score_name).fill_null(0).round(4).alias("score"),
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+ score_expr.fill_null(0.0).round(4).alias("score"),
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  ]
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  ).drop_nulls()
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@@ -228,14 +229,16 @@ def create_standardised_results(
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  ):
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  sort_order = SortOrder.ASCENDING if sort_order.lower() == "ascending" else SortOrder.DESCENDING
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  use_parquet = True if version.parse(exomiser_version) >= version.parse("15.0.0") else False
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- read_result = pl.read_parquet if use_parquet else pl.read_json
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  result_files = (
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  files_with_suffix(result_dir, ".parquet")
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  if use_parquet
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  else files_with_suffix(result_dir, ".json")
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  )
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  for exomiser_result_path in result_files:
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- exomiser_result = read_result(exomiser_result_path, infer_schema_length=None)
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+ if use_parquet:
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+ exomiser_result = pl.read_parquet(exomiser_result_path)
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+ else:
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+ exomiser_result = pl.read_json(exomiser_result_path, infer_schema_length=None)
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  if gene_analysis:
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  gene_results = (
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  extract_gene_results_from_parquet(exomiser_result, score_name)
{pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pheval_exomiser
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- Version: 0.4.3
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+ Version: 0.4.5
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  Summary:
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  Author: Yasemin Bridges
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  Author-email: y.bridges@qmul.ac.uk
@@ -52,9 +52,9 @@ A `config.yaml` should be located in the input directory and formatted like so:
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  ```yaml
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  tool: exomiser
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  tool_version: 13.2.0
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- variant_analysis: True
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- gene_analysis: True
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- disease_analysis: False
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+ variant_analysis: true
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+ gene_analysis: true
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+ disease_analysis: false
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  tool_specific_configuration_options:
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  environment: local
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  exomiser_software_directory: exomiser-cli-13.2.0
{pheval_exomiser-0.4.3.dist-info → pheval_exomiser-0.4.5.dist-info}/RECORD RENAMED
@@ -3,7 +3,7 @@ pheval_exomiser/cli.py,sha256=0SR1-L2sREEkFRfUPwYwkbSaBsz_L_Sxq1S4c9LQLJg,350
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  pheval_exomiser/constants.py,sha256=o_pLWF8kX74BqyTsAZa7twwSKzedLnpupCI90k_bMqY,517
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  pheval_exomiser/post_process/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pheval_exomiser/post_process/post_process.py,sha256=bGNLO0LlsG26oKtvL3mtlcBTDY5gynKh1BwNjmUaIgI,972
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- pheval_exomiser/post_process/post_process_results_format.py,sha256=3S5BO79NSiDmCC_wFyyQ4OK695MDiTBKyLsaGzyJpPA,12313
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+ pheval_exomiser/post_process/post_process_results_format.py,sha256=D-5Lh_prEUR-Mc_8_aBZJWBOhj8zyjdt723BHT0a9wY,12450
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  pheval_exomiser/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pheval_exomiser/prepare/create_batch_commands.py,sha256=G-2pRboJalW8MeXDwSHR1ZAuhNdQJdHjJPxOo0KBgPM,18930
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  pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=pFzieoZogiPhSquN2p7THcXuCBrzqANwqbWO0e6BPu4,2943
@@ -11,7 +11,7 @@ pheval_exomiser/prepare/write_application_properties.py,sha256=KmG7GvkQo8AhnhRyq
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  pheval_exomiser/run/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pheval_exomiser/run/run.py,sha256=n9cDv9E4d-NELCIY_v2UCrXqbWOo27TM2_9lPn-YOwI,8030
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  pheval_exomiser/runner.py,sha256=RqVobVJlOwcPzbO5gLjDtkGaygWdFT9VrlIvOmyBQPw,2706
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- pheval_exomiser-0.4.3.dist-info/METADATA,sha256=QVqcvOB24O5_jdKb6B2LJWrFkkLqUQXgyl0ShiQtWhY,7294
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- pheval_exomiser-0.4.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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- pheval_exomiser-0.4.3.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
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- pheval_exomiser-0.4.3.dist-info/RECORD,,
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+ pheval_exomiser-0.4.5.dist-info/METADATA,sha256=u8-_K3F7Zxk8Aqxd0rHfRorymeX1VZkOT4ud1N2Iojo,7294
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+ pheval_exomiser-0.4.5.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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+ pheval_exomiser-0.4.5.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
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+ pheval_exomiser-0.4.5.dist-info/RECORD,,