mgnify-pipelines-toolkit 1.2.1__tar.gz → 1.2.2__tar.gz

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  1. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/PKG-INFO +1 -1
  2. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +18 -17
  3. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/PKG-INFO +1 -1
  4. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/pyproject.toml +1 -1
  5. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/LICENSE +0 -0
  6. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/README.md +0 -0
  7. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/__init__.py +0 -0
  8. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/__init__.py +0 -0
  9. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +0 -0
  10. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py +0 -0
  11. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +0 -0
  12. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py +0 -0
  13. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py +0 -0
  14. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py +0 -0
  15. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py +0 -0
  16. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py +0 -0
  17. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py +0 -0
  18. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py +0 -0
  19. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py +0 -0
  20. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py +0 -0
  21. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py +0 -0
  22. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/go_utils.py +0 -0
  23. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py +0 -0
  24. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py +0 -0
  25. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py +0 -0
  26. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/study_summary_generator.py +0 -0
  27. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py +0 -0
  28. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py +0 -0
  29. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py +0 -0
  30. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/genomes/__init__.py +0 -0
  31. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/__init__.py +0 -0
  32. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py +0 -0
  33. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/dwc_summary_generator.py +0 -0
  34. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py +0 -0
  35. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +0 -0
  36. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py +0 -0
  37. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py +0 -0
  38. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py +0 -0
  39. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py +0 -0
  40. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/db_labels.py +0 -0
  41. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/ncrna.py +0 -0
  42. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/regex_fasta_header.py +0 -0
  43. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/tax_ranks.py +0 -0
  44. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/thresholds.py +0 -0
  45. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/constants/var_region_coordinates.py +0 -0
  46. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/schemas/schemas.py +0 -0
  47. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/utils/__init__.py +0 -0
  48. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/utils/fasta_to_delimited.py +0 -0
  49. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/utils/get_mpt_version.py +0 -0
  50. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt +0 -0
  51. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/dependency_links.txt +0 -0
  52. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/entry_points.txt +0 -0
  53. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/requires.txt +0 -0
  54. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/top_level.txt +0 -0
  55. {mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/setup.cfg +0 -0
{mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mgnify_pipelines_toolkit
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- Version: 1.2.1
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+ Version: 1.2.2
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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
{mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py RENAMED
@@ -300,23 +300,24 @@ def main():
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  if paired_end:
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  rev_fr.close()
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- ref_db = ""
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-
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- if len(taxa_df.columns) == 9:
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- tax_assignment_dict = make_tax_assignment_dict_silva(taxa_df, asv_dict)
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- ref_db = "silva"
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- elif len(taxa_df.columns) == 10:
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- tax_assignment_dict = make_tax_assignment_dict_pr2(taxa_df, asv_dict)
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- ref_db = "pr2"
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-
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- with open(f"./{sample}_{amp_region}_{ref_db}_asv_krona_counts.txt", "w") as fw:
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- for tax_assignment, count in tax_assignment_dict.items():
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- fw.write(f"{count}\t{tax_assignment}\n")
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-
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- asv_count_df = generate_asv_count_dict(asv_dict)
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- asv_count_df.to_csv(
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- f"./{sample}_{amp_region}_asv_read_counts.tsv", sep="\t", index=False
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- )
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+ if asv_dict: # if there are matches between taxonomic and ASV annotations
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+ ref_db = ""
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+
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+ if len(taxa_df.columns) == 9:
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+ tax_assignment_dict = make_tax_assignment_dict_silva(taxa_df, asv_dict)
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+ ref_db = "silva"
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+ elif len(taxa_df.columns) == 10:
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+ tax_assignment_dict = make_tax_assignment_dict_pr2(taxa_df, asv_dict)
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+ ref_db = "pr2"
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+
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+ with open(f"./{sample}_{amp_region}_{ref_db}_asv_krona_counts.txt", "w") as fw:
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+ for tax_assignment, count in tax_assignment_dict.items():
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+ fw.write(f"{count}\t{tax_assignment}\n")
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+
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+ asv_count_df = generate_asv_count_dict(asv_dict)
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+ asv_count_df.to_csv(
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+ f"./{sample}_{amp_region}_asv_read_counts.tsv", sep="\t", index=False
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+ )
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  if __name__ == "__main__":
{mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/mgnify_pipelines_toolkit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mgnify_pipelines_toolkit
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- Version: 1.2.1
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+ Version: 1.2.2
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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
{mgnify_pipelines_toolkit-1.2.1 → mgnify_pipelines_toolkit-1.2.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "mgnify_pipelines_toolkit"
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- version = "1.2.1"
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+ version = "1.2.2"
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  readme = "README.md"
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  license = { text = "Apache Software License 2.0" }
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  authors = [