mgnify-pipelines-toolkit 1.2.8__tar.gz → 1.2.9__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-1.2.9}/PKG-INFO +1 -1
  2. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py +4 -2
  3. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/PKG-INFO +1 -1
  4. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/pyproject.toml +1 -1
  5. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/LICENSE +0 -0
  6. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/README.md +0 -0
  7. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/__init__.py +0 -0
  8. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/__init__.py +0 -0
  9. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +0 -0
  10. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +0 -0
  11. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py +0 -0
  12. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/permute_primers.py +0 -0
  13. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +0 -0
  14. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py +0 -0
  15. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py +0 -0
  16. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py +0 -0
  17. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py +0 -0
  18. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py +0 -0
  19. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py +0 -0
  20. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py +0 -0
  21. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py +0 -0
  22. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py +0 -0
  23. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/go_utils.py +0 -0
  24. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py +0 -0
  25. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py +0 -0
  26. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py +0 -0
  27. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/study_summary_generator.py +0 -0
  28. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py +0 -0
  29. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py +0 -0
  30. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py +0 -0
  31. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/genomes/__init__.py +0 -0
  32. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/rawreads/study_summary_generator.py +0 -0
  33. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/__init__.py +0 -0
  34. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py +0 -0
  35. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/dwc_summary_generator.py +0 -0
  36. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py +0 -0
  37. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +0 -0
  38. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py +0 -0
  39. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py +0 -0
  40. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py +0 -0
  41. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py +0 -0
  42. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/db_labels.py +0 -0
  43. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/ncrna.py +0 -0
  44. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/regex_fasta_header.py +0 -0
  45. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/tax_ranks.py +0 -0
  46. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/thresholds.py +0 -0
  47. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/constants/var_region_coordinates.py +0 -0
  48. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/schemas/schemas.py +0 -0
  49. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/utils/__init__.py +0 -0
  50. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/utils/fasta_to_delimited.py +0 -0
  51. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit/utils/get_mpt_version.py +0 -0
  52. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt +0 -0
  53. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/dependency_links.txt +0 -0
  54. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/entry_points.txt +0 -0
  55. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/requires.txt +0 -0
  56. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/mgnify_pipelines_toolkit.egg-info/top_level.txt +0 -0
  57. {mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/setup.cfg +0 -0
{mgnify_pipelines_toolkit-1.2.8 → mgnify_pipelines_toolkit-1.2.9}/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: 1.2.9
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-1.2.9}/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-1.2.9}/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: 1.2.9
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-1.2.9}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "mgnify_pipelines_toolkit"
3
- version = "1.2.8"
3
+ version = "1.2.9"
4
4
  readme = "README.md"
5
5
  license = { text = "Apache Software License 2.0" }
6
6
  authors = [