pheval-exomiser 0.2.1__tar.gz → 0.2.2__tar.gz

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Files changed (17) hide show
  1. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/PKG-INFO +1 -1
  2. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/pyproject.toml +1 -1
  3. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/create_batch_commands.py +4 -2
  4. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/README.md +0 -0
  5. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/__init__.py +0 -0
  6. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/cli.py +0 -0
  7. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/constants.py +0 -0
  8. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/post_process/__init__.py +0 -0
  9. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/post_process/post_process.py +0 -0
  10. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/post_process/post_process_results_format.py +0 -0
  11. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/__init__.py +0 -0
  12. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/tool_specific_configuration_options.py +0 -0
  13. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/write_application_properties.py +0 -0
  14. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/yaml_to_family_phenopacket.py +0 -0
  15. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/run/__init__.py +0 -0
  16. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/run/run.py +0 -0
  17. {pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/runner.py +0 -0
{pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: pheval_exomiser
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- Version: 0.2.1
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+ Version: 0.2.2
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  Summary:
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  Author: Yasemin Bridges
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  Author-email: y.bridges@qmul.ac.uk
{pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "pheval_exomiser"
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- version = "0.2.1"
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+ version = "0.2.2"
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  description = ""
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  authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
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  "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
{pheval_exomiser-0.2.1 → pheval_exomiser-0.2.2}/src/pheval_exomiser/prepare/create_batch_commands.py RENAMED
@@ -7,7 +7,7 @@ from typing import Optional
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  import click
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  from phenopackets import Family, Phenopacket
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  from pheval.prepare.custom_exceptions import MutuallyExclusiveOptionError
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- from pheval.utils.file_utils import all_files, files_with_suffix, obtain_closest_file_name
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+ from pheval.utils.file_utils import all_files, files_with_suffix
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  from pheval.utils.phenopacket_utils import PhenopacketUtil, phenopacket_reader
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  from pheval_exomiser.constants import (
@@ -69,7 +69,9 @@ class CommandCreator:
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  return (
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  self.output_options_file
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  if self.output_options_dir_files is None
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- else obtain_closest_file_name(self.phenopacket_path, self.output_options_dir_files)
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+ else self.output_options_dir_files[0].parent.joinpath(
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+ self.phenopacket_path.stem + "-output_options.yml"
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+ )
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  )
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  def add_phenotype_only_arguments(self) -> ExomiserCommandLineArguments: