pheval-exomiser 0.3.0__py3-none-any.whl → 0.3.2__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.
- pheval_exomiser/post_process/post_process_results_format.py +1 -1
- pheval_exomiser/prepare/create_batch_commands.py +8 -2
- {pheval_exomiser-0.3.0.dist-info → pheval_exomiser-0.3.2.dist-info}/METADATA +4 -1
- {pheval_exomiser-0.3.0.dist-info → pheval_exomiser-0.3.2.dist-info}/RECORD +6 -6
- {pheval_exomiser-0.3.0.dist-info → pheval_exomiser-0.3.2.dist-info}/WHEEL +1 -1
- {pheval_exomiser-0.3.0.dist-info → pheval_exomiser-0.3.2.dist-info}/entry_points.txt +0 -0
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@@ -136,7 +136,7 @@ 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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for exomiser_json_result_path in files_with_suffix(result_dir, ".json"):
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exomiser_json_result = pl.read_json(exomiser_json_result_path)
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exomiser_json_result = pl.read_json(exomiser_json_result_path, infer_schema_length=None)
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if gene_analysis:
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gene_results = extract_gene_results_from_json(exomiser_json_result, score_name)
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generate_gene_result(
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@@ -100,8 +100,14 @@ class CommandCreator:
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)
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def add_variant_analysis_arguments(self, vcf_dir: Path) -> ExomiserCommandLineArguments:
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vcf_file_data =
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self.phenopacket_path, vcf_dir
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vcf_file_data = (
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PhenopacketUtil(self.phenopacket).vcf_file_data(self.phenopacket_path, vcf_dir)
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if vcf_dir.exists()
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else [
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file
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for file in self.phenopacket.files
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if file.file_attributes["fileFormat"] == "vcf"
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][0]
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)
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output_options_file = self.assign_output_options_file()
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if self.environment == "local":
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.3
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Name: pheval_exomiser
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Version: 0.3.
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Version: 0.3.2
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Summary:
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Author: Yasemin Bridges
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Author-email: y.bridges@qmul.ac.uk
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@@ -162,6 +162,9 @@ e.g.,
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└── vcf
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```
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> [!IMPORTANT]
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> If a `vcf` directory is not found in the testdata directory then the path to the VCF will be taken from the phenopacket if `variant_analysis` is set to True.
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## Run command
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Once the testdata and input directories are correctly configured for the run, the `pheval run` command can be executed.
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@@ -3,15 +3,15 @@ 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=2vkwe60Ptf7UuPCR2ShcI80-kn-1WaPDa74cCBTUKF0,968
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pheval_exomiser/post_process/post_process_results_format.py,sha256=
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pheval_exomiser/post_process/post_process_results_format.py,sha256=8fmiPy4xJjhe6ajTlJEYx2na0EeJftkTuYQCzv5uIJk,8458
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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=
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pheval_exomiser/prepare/create_batch_commands.py,sha256=R06cn1c5pf_agUQfrFUQ2KEo8il0Z4fJntS2HKYCQXw,17410
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pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=4gedZ9iadRXK6tF9P-ju-dhj8-F2-fhrXVhfYIsAxFQ,2922
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pheval_exomiser/prepare/write_application_properties.py,sha256=KmG7GvkQo8AhnhRyqohTFvqjfhEhbcs78UYYoigxJ3w,8933
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pheval_exomiser/run/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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pheval_exomiser/run/run.py,sha256=bK_gL52zRl71Lxe-i-P6L4-dMstxFAG6SVNPO6G823o,7109
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pheval_exomiser/runner.py,sha256=3-0kec2yzQoZNpqZXSBIWBD1QR24s_BmHGCLXmP4fos,2620
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pheval_exomiser-0.3.
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pheval_exomiser-0.3.
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pheval_exomiser-0.3.
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pheval_exomiser-0.3.
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pheval_exomiser-0.3.2.dist-info/METADATA,sha256=ioOgpn28cmb8KjyzrO3Zuk2JD-E9LF_l6A39GDzC7E8,7641
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pheval_exomiser-0.3.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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pheval_exomiser-0.3.2.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
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pheval_exomiser-0.3.2.dist-info/RECORD,,
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File without changes
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