ssi-analysis-result-parsers 0.0.11__tar.gz → 0.0.12__tar.gz

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.
Files changed (63) hide show
  1. {ssi_analysis_result_parsers-0.0.11/ssi_analysis_result_parsers.egg-info → ssi_analysis_result_parsers-0.0.12}/PKG-INFO +3 -3
  2. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/settings.ini +3 -3
  3. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/Nmeningitidis_parser.py +7 -2
  4. ssi_analysis_result_parsers-0.0.12/ssi_analysis_result_parsers/__init__.py +1 -0
  5. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12/ssi_analysis_result_parsers.egg-info}/PKG-INFO +3 -3
  6. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/top_level.txt +1 -0
  7. ssi_analysis_result_parsers-0.0.11/ssi_analysis_result_parsers/__init__.py +0 -1
  8. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/LICENSE +0 -0
  9. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/MANIFEST.in +0 -0
  10. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/README.md +0 -0
  11. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/pyproject.toml +0 -0
  12. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/setup.cfg +0 -0
  13. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/setup.py +0 -0
  14. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/Ecoli_parser.py +0 -0
  15. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/Legionella_parser.py +0 -0
  16. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/Spyogenes_parser.py +0 -0
  17. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/_modidx.py +0 -0
  18. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/blast_parser.py +0 -0
  19. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/config/config.default.env +0 -0
  20. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/config/config.default.yaml +0 -0
  21. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/core.py +0 -0
  22. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/hello_world.py +0 -0
  23. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/some_string.py +0 -0
  24. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/SOURCES.txt +0 -0
  25. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/dependency_links.txt +0 -0
  26. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/entry_points.txt +0 -0
  27. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/not-zip-safe +0 -0
  28. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/requires.txt +2 -2
  29. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/.DS_Store +0 -0
  30. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Ecoli/ERR14229029.res +0 -0
  31. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Ecoli/ERR3528110.res +0 -0
  32. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Ecoli/samplesheet.tsv +0 -0
  33. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/batch_parser_file_paths.tsv +0 -0
  34. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/lag-1_blast.tsv +0 -0
  35. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/lag-1_blast_2.tsv +0 -0
  36. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/test.sbt.tsv +0 -0
  37. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/test.tsv +0 -0
  38. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Legionella/test2.sbt.tsv +0 -0
  39. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Nmeningitidis/batch_parser_file_paths.tsv +0 -0
  40. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Nmeningitidis/meningotype/meningotype1.tsv +0 -0
  41. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Nmeningitidis/meningotype/meningotype2.tsv +0 -0
  42. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Nmeningitidis/meningotype/meningotype3.tsv +0 -0
  43. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Nmeningitidis/neisseria_mlst_scheme.tsv +0 -0
  44. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/batch_parser_file_paths.tsv +0 -0
  45. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/Mga.fasta +0 -0
  46. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/emm_clusters.txt +0 -0
  47. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test1.emm.blast.tsv +0 -0
  48. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test1.mga.blast.tsv +0 -0
  49. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test2.emm.blast.tsv +0 -0
  50. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test2.mga.blast.tsv +0 -0
  51. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test3.emm.blast.tsv +0 -0
  52. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test4.emm.blast.tsv +0 -0
  53. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test5.emm.blast.tsv +0 -0
  54. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test6.emm.blast.tsv +0 -0
  55. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/Spyogenes/emm_typing/test7.emm.blast.tsv +0 -0
  56. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/blast_parser/allele_matches_test.tsv +0 -0
  57. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/blast_parser/empty_gene_presence_absense_test.tsv +0 -0
  58. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/blast_parser/gene_presence_absence_test.tsv +0 -0
  59. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_input/empty_file.txt +0 -0
  60. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_output/Ecoli/KMA_cases_parser.tsv +0 -0
  61. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_output/output_with_sample_name.tsv +0 -0
  62. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_output/test.tsv +0 -0
  63. {ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/test_output/test_batch_output.tsv +0 -0
{ssi_analysis_result_parsers-0.0.11/ssi_analysis_result_parsers.egg-info → ssi_analysis_result_parsers-0.0.12}/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: 0.0.11
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+ Version: 0.0.12
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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
@@ -19,9 +19,9 @@ Requires-Python: >=3.9
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: fastcore
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- Requires-Dist: python_dotenv
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- Requires-Dist: envyaml
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  Requires-Dist: pandas
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+ Requires-Dist: envyaml
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+ Requires-Dist: python_dotenv
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  Requires-Dist: black
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  Provides-Extra: dev
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  Dynamic: author
{ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/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 = 0.0.11
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+ version = 0.0.12
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  min_python = 3.9
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  license = MIT
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  black_formatting = True
@@ -44,8 +44,8 @@ user = thej-ssi
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  # console_scripts =
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  # conda_user =
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  # package_data =
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- requirements = fastcore
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- pip_requirements = python_dotenv envyaml pandas black
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+ requirements = fastcore pandas envyaml
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+ pip_requirements = python_dotenv black
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  console_scripts =
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  blast_parser_presence_absence=ssi_analysis_result_parsers.blast_parser:presence_absence
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  blast_parser_allele_matches=ssi_analysis_result_parsers.blast_parser:allele_matches
{ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers/Nmeningitidis_parser.py RENAMED
@@ -42,10 +42,15 @@ def extract_meningotype(meningotype_tsv: Path):
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  try:
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  df = pandas.read_csv(meningotype_tsv, sep="\t")
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  PorA_split = df["PorA"][0].split(",")
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+ VR1 = PorA_split[0]
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+ try:
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+ VR2 = PorA_split[1]
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+ except:
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+ VR2 = ""
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  return {
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  "SEROGROUP": df["SEROGROUP"][0],
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- "VR1": PorA_split[0],
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- "VR2": PorA_split[1],
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+ "VR1": VR1,
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+ "VR2": VR2,
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  "FetA": df["FetA"][0],
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  }
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  except pandas.errors.EmptyDataError:
ssi_analysis_result_parsers-0.0.12/ssi_analysis_result_parsers/__init__.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "0.0.11"
{ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12/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: 0.0.11
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+ Version: 0.0.12
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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
@@ -19,9 +19,9 @@ Requires-Python: >=3.9
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: fastcore
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- Requires-Dist: python_dotenv
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- Requires-Dist: envyaml
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  Requires-Dist: pandas
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+ Requires-Dist: envyaml
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+ Requires-Dist: python_dotenv
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  Requires-Dist: black
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  Provides-Extra: dev
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  Dynamic: author
ssi_analysis_result_parsers-0.0.11/ssi_analysis_result_parsers/__init__.py DELETED
@@ -1 +0,0 @@
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- __version__ = "0.0.10"
{ssi_analysis_result_parsers-0.0.11 → ssi_analysis_result_parsers-0.0.12}/ssi_analysis_result_parsers.egg-info/requires.txt RENAMED
@@ -1,7 +1,7 @@
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  fastcore
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- python_dotenv
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- envyaml
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  pandas
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+ envyaml
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+ python_dotenv
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  black
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  [dev]