ssi-analysis-result-parsers 0.0.2__tar.gz → 0.0.4__tar.gz

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Files changed (37) hide show
  1. {ssi_analysis_result_parsers-0.0.2/ssi_analysis_result_parsers.egg-info → ssi_analysis_result_parsers-0.0.4}/PKG-INFO +1 -1
  2. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/settings.ini +1 -1
  3. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/Legionella_parser.py +2 -1
  4. ssi_analysis_result_parsers-0.0.4/ssi_analysis_result_parsers/__init__.py +1 -0
  5. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/core.py +1 -0
  6. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4/ssi_analysis_result_parsers.egg-info}/PKG-INFO +1 -1
  7. ssi_analysis_result_parsers-0.0.2/ssi_analysis_result_parsers/__init__.py +0 -1
  8. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/LICENSE +0 -0
  9. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/MANIFEST.in +0 -0
  10. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/README.md +0 -0
  11. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/pyproject.toml +0 -0
  12. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/setup.cfg +0 -0
  13. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/setup.py +0 -0
  14. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/_modidx.py +0 -0
  15. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/blast_parser.py +0 -0
  16. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/config/config.default.env +0 -0
  17. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/config/config.default.yaml +0 -0
  18. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/hello_world.py +0 -0
  19. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/some_string.py +0 -0
  20. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/SOURCES.txt +0 -0
  21. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/dependency_links.txt +0 -0
  22. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/entry_points.txt +0 -0
  23. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/not-zip-safe +0 -0
  24. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/requires.txt +0 -0
  25. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers.egg-info/top_level.txt +0 -0
  26. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/.DS_Store +0 -0
  27. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/Legionella/batch_parser_file_paths.tsv +0 -0
  28. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/Legionella/lag-1_blast.tsv +0 -0
  29. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/Legionella/lag-1_blast_2.tsv +0 -0
  30. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/Legionella/test.sbt.tsv +0 -0
  31. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/Legionella/test2.sbt.tsv +0 -0
  32. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/blast_parser/allele_matches_test.tsv +0 -0
  33. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/blast_parser/empty_gene_presence_absense_test.tsv +0 -0
  34. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_input/blast_parser/gene_presence_absence_test.tsv +0 -0
  35. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_output/output_with_sample_name.tsv +0 -0
  36. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_output/test.tsv +0 -0
  37. {ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/test_output/test_batch_output.tsv +0 -0
{ssi_analysis_result_parsers-0.0.2/ssi_analysis_result_parsers.egg-info → ssi_analysis_result_parsers-0.0.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ssi_analysis_result_parsers
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- Version: 0.0.2
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+ Version: 0.0.4
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  Summary: TODO
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  Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
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  Author: Thor Bech Johannesen
{ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/settings.ini RENAMED
@@ -5,7 +5,7 @@
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  ### Python library ###
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  repo = ssi_analysis_result_parsers
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  lib_name = %(repo)s
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- version = 0.0.2
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+ version = 0.0.4
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  min_python = 3.9
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  license = MIT
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  black_formatting = True
{ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/Legionella_parser.py RENAMED
@@ -65,6 +65,8 @@ def legionella_summary(legionella_sbt_results_tsv: Path, lag1_blast_tsv: Path) -
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  results_dict = core.update_results_dict(
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  sbt_results_dict, lag1_blast_dict, old_duplicate_key_prefix="SBT: "
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  )
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+ if results_dict is None:
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+ return {}
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  return results_dict
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@@ -145,7 +147,6 @@ class LegionellaResults(core.PipelineResults):
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  include_match_stats=False,
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  gene_names=["lag-1"],
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  )
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- print(lag1_blast_dict)
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  results_dict = core.update_results_dict(
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  sbt_results_dict, lag1_blast_dict, old_duplicate_key_prefix="SBT: "
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  )
ssi_analysis_result_parsers-0.0.4/ssi_analysis_result_parsers/__init__.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "0.0.3"
{ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4}/ssi_analysis_result_parsers/core.py RENAMED
@@ -196,6 +196,7 @@ def get_samplesheet(sample_sheet_config: dict) -> pd.DataFrame:
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  class PipelineResults:
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  def __init__(self, results_dict):
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+ print(results_dict)
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  self.results_dict = results_dict
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  self.results_df = pandas.DataFrame.from_dict(results_dict, orient="index")
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{ssi_analysis_result_parsers-0.0.2 → ssi_analysis_result_parsers-0.0.4/ssi_analysis_result_parsers.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ssi_analysis_result_parsers
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- Version: 0.0.2
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+ Version: 0.0.4
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  Summary: TODO
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  Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
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  Author: Thor Bech Johannesen
ssi_analysis_result_parsers-0.0.2/ssi_analysis_result_parsers/__init__.py DELETED
@@ -1 +0,0 @@
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- __version__ = "0.0.2"