mgnify-pipelines-toolkit 0.2.1__tar.gz → 0.2.2__tar.gz

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  1. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/PKG-INFO +2 -1
  2. mgnify_pipelines_toolkit-0.2.2/mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py +829 -0
  3. mgnify_pipelines_toolkit-0.2.2/mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py +82 -0
  4. mgnify_pipelines_toolkit-0.2.2/mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py +170 -0
  5. mgnify_pipelines_toolkit-0.2.2/mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py +243 -0
  6. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/thresholds.py +7 -0
  7. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/PKG-INFO +2 -1
  8. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt +4 -0
  9. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/entry_points.txt +2 -1
  10. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/requires.txt +1 -0
  11. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/pyproject.toml +5 -3
  12. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/LICENSE +0 -0
  13. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/README.md +0 -0
  14. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/__init__.py +0 -0
  15. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/__init__.py +0 -0
  16. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py +0 -0
  17. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py +0 -0
  18. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py +0 -0
  19. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py +0 -0
  20. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +0 -0
  21. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py +0 -0
  22. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +0 -0
  23. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py +0 -0
  24. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +0 -0
  25. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py +0 -0
  26. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py +0 -0
  27. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_matching.py +0 -0
  28. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py +0 -0
  29. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py +0 -0
  30. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/cgc_merge.py +0 -0
  31. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py +0 -0
  32. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/go_utils.py +0 -0
  33. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py +0 -0
  34. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/__init__.py +0 -0
  35. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py +0 -0
  36. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +0 -0
  37. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py +0 -0
  38. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py +0 -0
  39. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py +0 -0
  40. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/analysis/shared/study_summary_generator.py +0 -0
  41. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/db_labels.py +0 -0
  42. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/regex_ambiguous_bases.py +0 -0
  43. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/regex_fasta_header.py +0 -0
  44. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/tax_ranks.py +0 -0
  45. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/constants/var_region_coordinates.py +0 -0
  46. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/schemas/schemas.py +0 -0
  47. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/utils/__init__.py +0 -0
  48. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/utils/fasta_to_delimited.py +0 -0
  49. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit/utils/get_mpt_version.py +0 -0
  50. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/dependency_links.txt +0 -0
  51. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/mgnify_pipelines_toolkit.egg-info/top_level.txt +0 -0
  52. {mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/setup.cfg +0 -0
{mgnify_pipelines_toolkit-0.2.1 → mgnify_pipelines_toolkit-0.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: mgnify_pipelines_toolkit
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- Version: 0.2.1
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+ Version: 0.2.2
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  Summary: Collection of scripts and tools for MGnify pipelines
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  Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
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  License: Apache Software License 2.0
@@ -30,6 +30,7 @@ Requires-Dist: regex==2023.12.25; extra == "tests"
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  Requires-Dist: requests==2.32.3; extra == "tests"
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  Requires-Dist: click==8.1.7; extra == "tests"
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  Requires-Dist: pandera==0.22.1; extra == "tests"
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+ Requires-Dist: pyfastx>=2.2.0; extra == "tests"
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  Provides-Extra: dev
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  Requires-Dist: mgnify_pipelines_toolkit[tests]; extra == "dev"
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  Requires-Dist: pre-commit==3.8.0; extra == "dev"