rdrpcatch 0.0.2__tar.gz → 0.0.3__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 (87) hide show
  1. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/PKG-INFO +1 -1
  2. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/pyproject.toml +1 -1
  3. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_wrapper.py +2 -2
  4. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.gitignore +0 -0
  5. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/.gitignore +0 -0
  6. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/.name +0 -0
  7. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/ColaB-Scan.iml +0 -0
  8. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/inspectionProfiles/profiles_settings.xml +0 -0
  9. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/misc.xml +0 -0
  10. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/modules.xml +0 -0
  11. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/vcs.xml +0 -0
  12. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/workspace.xml +0 -0
  13. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/LICENSE +0 -0
  14. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/README.md +0 -0
  15. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/dependencies/rdrpcatch_test_env.yaml +0 -0
  16. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/dependencies/requirements.txt +0 -0
  17. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/images/rdrpcatch_flowchart_v0.png +0 -0
  18. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/meta.yaml +0 -0
  19. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/__init__.py +0 -0
  20. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/cli/__init__.py +0 -0
  21. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/cli/args.py +0 -0
  22. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/__init__.py +0 -0
  23. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/fetch_dbs.py +0 -0
  24. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/format_pyhmmer_out.py +0 -0
  25. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/gui.py +0 -0
  26. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/mmseqs_tax.py +0 -0
  27. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/paths.py +0 -0
  28. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/plot.py +0 -0
  29. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/run_pyhmmer.py +0 -0
  30. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/run_seqkit.py +0 -0
  31. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_scripts/utils.py +0 -0
  32. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/meta_4test.yaml +0 -0
  33. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch-1.0.0-py312_2.tar.bz2 +0 -0
  34. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_env.yaml +0 -0
  35. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_gff_files/test_translate_full_aminoacid_rdrpcatch.gff3 +0 -0
  36. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_fasta/test_translate_full_aminoacid_contigs.fasta +0 -0
  37. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_fasta/test_translate_trimmed_aminoacid_contigs.fasta +0 -0
  38. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_output_annotated.tsv +0 -0
  39. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_ID_score_plot.html +0 -0
  40. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_contig_coverage_plot.html +0 -0
  41. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_evalue_plot.html +0 -0
  42. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_norm_bitscore_contig_plot.html +0 -0
  43. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_norm_bitscore_plot_profile.html +0 -0
  44. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_profile_coverage_plot.html +0 -0
  45. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_score_plot.html +0 -0
  46. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/test_translate_rdrpcatch_plots/test_translate_upset_plot.png +0 -0
  47. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_Lucaprot_hmm_output_best_hit.txt +0 -0
  48. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_NeoRdRp.2.1_hmm_output_best_hit.txt +0 -0
  49. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_NeoRdRp_hmm_output_best_hit.txt +0 -0
  50. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_RDRP-scan_hmm_output_best_hit.txt +0 -0
  51. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_RVMT_hmm_output_best_hit.txt +0 -0
  52. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_TSA_Olendraite_fam_hmm_output_best_hit.txt +0 -0
  53. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/best_hit_hmm_output/test_translate_TSA_Olendraite_gen_hmm_output_best_hit.txt +0 -0
  54. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_Lucaprot_hmm_output_formatted.txt +0 -0
  55. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_NeoRdRp.2.1_hmm_output_formatted.txt +0 -0
  56. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_NeoRdRp_hmm_output_formatted.txt +0 -0
  57. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_RDRP-scan_hmm_output_formatted.txt +0 -0
  58. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_RVMT_hmm_output_formatted.txt +0 -0
  59. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_TSA_Olendraite_fam_hmm_output_formatted.txt +0 -0
  60. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/formatted_hmm_output/test_translate_TSA_Olendraite_gen_hmm_output_formatted.txt +0 -0
  61. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_Lucaprot_hmmsearch_output.custom.tsv +0 -0
  62. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_Lucaprot_hmmsearch_output.txt +0 -0
  63. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_NeoRdRp.2.1_hmmsearch_output.custom.tsv +0 -0
  64. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_NeoRdRp.2.1_hmmsearch_output.txt +0 -0
  65. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_NeoRdRp_hmmsearch_output.custom.tsv +0 -0
  66. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_NeoRdRp_hmmsearch_output.txt +0 -0
  67. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_RDRP-scan_hmmsearch_output.custom.tsv +0 -0
  68. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_RDRP-scan_hmmsearch_output.txt +0 -0
  69. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_RVMT_hmmsearch_output.custom.tsv +0 -0
  70. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_RVMT_hmmsearch_output.txt +0 -0
  71. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_TSA_Olendraite_fam_hmmsearch_output.custom.tsv +0 -0
  72. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_TSA_Olendraite_fam_hmmsearch_output.txt +0 -0
  73. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_TSA_Olendraite_gen_hmmsearch_output.custom.tsv +0 -0
  74. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/hmm_output/test_translate_TSA_Olendraite_gen_hmmsearch_output.txt +0 -0
  75. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_e_search_output/test_translate_mmseqs_e_search.tsv +0 -0
  76. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_tax_output/test_translate_mmseqs_tax_lca.tsv +0 -0
  77. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_tax_output/test_translate_mmseqs_tax_report +0 -0
  78. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_tax_output/test_translate_mmseqs_tax_tophit_aln +0 -0
  79. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_tax_output/test_translate_mmseqs_tax_tophit_report +0 -0
  80. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/mmseqs_tax_output/tmp/16608414482057878997/easy-taxonomy.sh +0 -0
  81. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/test_translate_logs/test_translate_mmseqs_e_search.log +0 -0
  82. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/test_translate_logs/test_translate_mmseqs_tax.log +0 -0
  83. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/test_translate_logs/test_translate_rdrpcatch.log +0 -0
  84. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/tsv_files/test_translate_combined.tsv +0 -0
  85. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/tsv_files/test_translate_rdrpcatch_output.tsv +0 -0
  86. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/rdrpcatch_test_translate/tmp/tsv_files/test_translate_upset_data.tsv +0 -0
  87. {rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/testing/test_translate.fasta +0 -0
{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: rdrpcatch
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- Version: 0.0.2
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+ Version: 0.0.3
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  Dynamic: Summary
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  Project-URL: Home, https://github.com/dimitris-karapliafis/RdRpCATCH
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  Project-URL: Source, https://github.com/dimitris-karapliafis/RdRpCATCH
{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
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  [project]
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  name = "rdrpcatch"
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- version = "0.0.2"
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+ version = "0.0.3"
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  authors = [
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  {name = "Dimitris Karapliafis", email = "dimitris.karapliafis@wur.nl"},
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  {name = "Uri Neri", email = "uneri@lbl.gov"},
{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/rdrpcatch/rdrpcatch_wrapper.py RENAMED
@@ -458,7 +458,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
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  outputs.mmseqs_e_search_output_path, 7, cpus, outputs.mmseqs_e_search_log_path).run_mmseqs_e_search()
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  utils.mmseqs_parser(outputs.mmseqs_tax_output_lca_path, outputs.mmseqs_e_search_output_path).tax_to_rdrpcatch(
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- outputs.rdrpcatch_output, outputs.extended_rdrpcatch_output, seq_type)
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+ outputs.rdrpcatch_output_tsv, outputs.extended_rdrpcatch_output, seq_type)
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  elif seq_type == 'prot':
@@ -622,7 +622,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
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  outputs.mmseqs_e_search_output_path, 7, cpus, outputs.mmseqs_e_search_log_path).run_mmseqs_e_search()
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  utils.mmseqs_parser(outputs.mmseqs_tax_output_lca_path, outputs.mmseqs_e_search_output_path).tax_to_rdrpcatch(
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- outputs.rdrpcatch_output, outputs.extended_rdrpcatch_output, seq_type)
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+ outputs.rdrpcatch_output_tsv, outputs.extended_rdrpcatch_output, seq_type)
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  end_time = logger.stop_timer(start_time, verbose)
{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.gitignore RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/.gitignore RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/.name RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/misc.xml RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/modules.xml RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/vcs.xml RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/.idea/workspace.xml RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/LICENSE RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/README.md RENAMED
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{rdrpcatch-0.0.2 → rdrpcatch-0.0.3}/meta.yaml RENAMED
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