mgnify-pipelines-toolkit 1.2.8__tar.gz → 1.2.10__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.

Potentially problematic release.

This version of mgnify-pipelines-toolkit might be problematic. Click here for more details.

Files changed (57) hide show
  1. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/PKG-INFO +1 -1
  2. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py +4 -2
  3. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/schemas/schemas.py +2 -1
  4. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/PKG-INFO +1 -1
  5. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/pyproject.toml +1 -1
  6. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/LICENSE +0 -0
  7. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/README.md +0 -0
  8. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/__init__.py +0 -0
  9. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/__init__.py +0 -0
  10. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +0 -0
  11. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +0 -0
  12. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py +0 -0
  13. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/permute_primers.py +0 -0
  14. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +0 -0
  15. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py +0 -0
  16. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py +0 -0
  17. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py +0 -0
  18. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py +0 -0
  19. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py +0 -0
  20. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py +0 -0
  21. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py +0 -0
  22. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py +0 -0
  23. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py +0 -0
  24. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/go_utils.py +0 -0
  25. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py +0 -0
  26. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py +0 -0
  27. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py +0 -0
  28. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/study_summary_generator.py +0 -0
  29. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py +0 -0
  30. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py +0 -0
  31. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py +0 -0
  32. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/genomes/__init__.py +0 -0
  33. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/rawreads/study_summary_generator.py +0 -0
  34. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/__init__.py +0 -0
  35. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py +0 -0
  36. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/dwc_summary_generator.py +0 -0
  37. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py +0 -0
  38. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +0 -0
  39. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py +0 -0
  40. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py +0 -0
  41. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py +0 -0
  42. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py +0 -0
  43. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/db_labels.py +0 -0
  44. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/ncrna.py +0 -0
  45. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/regex_fasta_header.py +0 -0
  46. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/tax_ranks.py +0 -0
  47. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/thresholds.py +0 -0
  48. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/constants/var_region_coordinates.py +0 -0
  49. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/utils/__init__.py +0 -0
  50. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/utils/fasta_to_delimited.py +0 -0
  51. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/utils/get_mpt_version.py +0 -0
  52. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt +0 -0
  53. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/dependency_links.txt +0 -0
  54. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/entry_points.txt +0 -0
  55. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/requires.txt +0 -0
  56. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/top_level.txt +0 -0
  57. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/setup.cfg +0 -0
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: mgnify_pipelines_toolkit
3
- Version: 1.2.8
3
+ Version: 1.2.10
4
4
  Summary: Collection of scripts and tools for MGnify pipelines
5
5
  Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
6
6
  License: Apache Software License 2.0
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py RENAMED
@@ -89,8 +89,10 @@ def main():
89
89
  if iter_cds and feature["type"] == "CDS":
90
90
  # Annotate CDS features
91
91
 
92
- start = int(feature["location"].split(":")[0][1:])
93
- end = int(feature["location"].split(":")[1].split("]")[0])
92
+ # The > and < are removed to work with pseudogene outputs in Bakta
93
+ # A feature["location"] example that can be seen in Bakta outputs: "[81883:>82231](+)"
94
+ start = int(feature["location"].split(":")[0][1:].lstrip("<>"))
95
+ end = int(feature["location"].split(":")[1].split("]")[0].lstrip("<>"))
94
96
  strand = feature["location"].split("(")[1][0] # + or -
95
97
 
96
98
  if not region_name or not (region_start <= end and start <= region_end):
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit/schemas/schemas.py RENAMED
@@ -72,12 +72,13 @@ class INSDCRunAccession(RootModel):
72
72
 
73
73
 
74
74
  class AmpliconResultTypes(StrEnum):
75
- """Class that models the two allowed statuses for successful amplicon analysis runs.
75
+ """Class that models the three allowed statuses for successful amplicon analysis runs.
76
76
  Pydantic validates Enums very simply without needing to declare a new function.
77
77
  """
78
78
 
79
79
  all_results = "all_results"
80
80
  no_asvs = "no_asvs"
81
+ dada2_stats_fail = "dada2_stats_fail"
81
82
 
82
83
 
83
84
  class AmpliconPassedRunsRecord(BaseModel):
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/mgnify_pipelines_toolkit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: mgnify_pipelines_toolkit
3
- Version: 1.2.8
3
+ Version: 1.2.10
4
4
  Summary: Collection of scripts and tools for MGnify pipelines
5
5
  Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
6
6
  License: Apache Software License 2.0
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.10}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "mgnify_pipelines_toolkit"
3
- version = "1.2.8"
3
+ version = "1.2.10"
4
4
  readme = "README.md"
5
5
  license = { text = "Apache Software License 2.0" }
6
6
  authors = [