phykit 2.0.1__tar.gz → 2.0.2__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 (72) hide show
  1. {phykit-2.0.1 → phykit-2.0.2}/PKG-INFO +12 -5
  2. {phykit-2.0.1 → phykit-2.0.2}/README.md +2 -3
  3. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/dna_threader.py +15 -6
  4. phykit-2.0.2/phykit/version.py +1 -0
  5. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/PKG-INFO +12 -5
  6. phykit-2.0.1/phykit/version.py +0 -1
  7. {phykit-2.0.1 → phykit-2.0.2}/LICENSE.md +0 -0
  8. {phykit-2.0.1 → phykit-2.0.2}/phykit/__init__.py +0 -0
  9. {phykit-2.0.1 → phykit-2.0.2}/phykit/__main__.py +0 -0
  10. {phykit-2.0.1 → phykit-2.0.2}/phykit/helpers/__init__.py +0 -0
  11. {phykit-2.0.1 → phykit-2.0.2}/phykit/helpers/boolean_argument_parsing.py +0 -0
  12. {phykit-2.0.1 → phykit-2.0.2}/phykit/helpers/files.py +0 -0
  13. {phykit-2.0.1 → phykit-2.0.2}/phykit/helpers/stats_summary.py +0 -0
  14. {phykit-2.0.1 → phykit-2.0.2}/phykit/phykit.py +0 -0
  15. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/__init__.py +0 -0
  16. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/__init__.py +0 -0
  17. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/alignment_length.py +0 -0
  18. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/alignment_length_no_gaps.py +0 -0
  19. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/alignment_recoding.py +0 -0
  20. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/base.py +0 -0
  21. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/column_score.py +0 -0
  22. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/compositional_bias_per_site.py +0 -0
  23. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/create_concatenation_matrix.py +0 -0
  24. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/evolutionary_rate_per_site.py +0 -0
  25. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/faidx.py +0 -0
  26. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/gc_content.py +0 -0
  27. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/pairwise_identity.py +0 -0
  28. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/parsimony_informative_sites.py +0 -0
  29. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/rcv.py +0 -0
  30. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/rcvt.py +0 -0
  31. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/rename_fasta_entries.py +0 -0
  32. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/sum_of_pairs_score.py +0 -0
  33. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/variable_sites.py +0 -0
  34. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/base.py +0 -0
  35. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/__init__.py +0 -0
  36. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/base.py +0 -0
  37. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/bipartition_support_stats.py +0 -0
  38. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/branch_length_multiplier.py +0 -0
  39. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/collapse_branches.py +0 -0
  40. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/covarying_evolutionary_rates.py +0 -0
  41. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/dvmc.py +0 -0
  42. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/evolutionary_rate.py +0 -0
  43. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/hidden_paralogy_check.py +0 -0
  44. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/internal_branch_stats.py +0 -0
  45. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/internode_labeler.py +0 -0
  46. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/last_common_ancestor_subtree.py +0 -0
  47. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/lb_score.py +0 -0
  48. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/monophyly_check.py +0 -0
  49. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/nearest_neighbor_interchange.py +0 -0
  50. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/patristic_distances.py +0 -0
  51. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/polytomy_test.py +0 -0
  52. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/print_tree.py +0 -0
  53. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/prune_tree.py +0 -0
  54. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/rename_tree_tips.py +0 -0
  55. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/rf_distance.py +0 -0
  56. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/root_tree.py +0 -0
  57. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/saturation.py +0 -0
  58. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/spurious_sequence.py +0 -0
  59. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/terminal_branch_stats.py +0 -0
  60. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/tip_labels.py +0 -0
  61. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/tip_to_tip_distance.py +0 -0
  62. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/tip_to_tip_node_distance.py +0 -0
  63. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/total_tree_length.py +0 -0
  64. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/treeness.py +0 -0
  65. {phykit-2.0.1 → phykit-2.0.2}/phykit/services/tree/treeness_over_rcv.py +0 -0
  66. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/SOURCES.txt +0 -0
  67. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/dependency_links.txt +0 -0
  68. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/entry_points.txt +0 -0
  69. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/requires.txt +0 -0
  70. {phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/top_level.txt +0 -0
  71. {phykit-2.0.1 → phykit-2.0.2}/setup.cfg +0 -0
  72. {phykit-2.0.1 → phykit-2.0.2}/setup.py +0 -0
{phykit-2.0.1 → phykit-2.0.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: phykit
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- Version: 2.0.1
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+ Version: 2.0.2
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  Home-page: https://github.com/jlsteenwyk/phykit
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  Author: Jacob L. Steenwyk
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  Author-email: jlsteenwyk@gmail.com
@@ -18,6 +18,14 @@ Requires-Dist: numpy>=1.24.0
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  Requires-Dist: scipy>=1.11.3
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  Requires-Dist: scikit-learn>=1.4.2
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  Requires-Dist: cython
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: license-file
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+ Dynamic: requires-dist
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  <p align="center">
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  <a href="https://github.com/jlsteenwyk/phykit">
@@ -40,9 +48,8 @@ Requires-Dist: cython
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  <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
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  <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
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  </a>
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- <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
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- <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
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- alt="follow on Twitter">
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+ <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
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+ <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
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  </a>
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  <br />
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  <a href="https://pepy.tech/badge/phykit">
{phykit-2.0.1 → phykit-2.0.2}/README.md RENAMED
@@ -19,9 +19,8 @@
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  <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
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  <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
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  </a>
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- <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
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- <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
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- alt="follow on Twitter">
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+ <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
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+ <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
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  </a>
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  <br />
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  <a href="https://pepy.tech/badge/phykit">
{phykit-2.0.1 → phykit-2.0.2}/phykit/services/alignment/dna_threader.py RENAMED
@@ -49,12 +49,21 @@ class DNAThreader(Alignment):
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  # triplicate each amino acid
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  return ''.join(c * 3 for c in p_seq)
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- def normalize_n_seq(self, n_seq: Seq, normalized_p_seq: str) -> str:
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- # insert gaps at corresponding positions in the nucleotide sequence based on the protein sequence
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- normalized_n_seq = list(n_seq)
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- for idx, c in enumerate(normalized_p_seq):
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- if c in "-?*Xx":
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- normalized_n_seq.insert(idx, "-")
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+ def normalize_n_seq(self, n_seq: Seq, p_seq: Seq) -> str:
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+ codons = [str(n_seq[i:i+3]) for i in range(0, len(n_seq), 3)]
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+ normalized_n_seq = []
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+
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+ codon_idx = 0
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+ for aa in p_seq:
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+ if aa in "-?*Xx":
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+ normalized_n_seq.append("---")
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+ else:
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+ if codon_idx < len(codons):
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+ normalized_n_seq.append(codons[codon_idx])
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+ codon_idx += 1
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+ else:
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+ normalized_n_seq.append("---") # fallback in case of misalignment
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+
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  return ''.join(normalized_n_seq)
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  def thread(self, prot_records) -> Dict[str, str]:
phykit-2.0.2/phykit/version.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "2.0.2"
{phykit-2.0.1 → phykit-2.0.2}/phykit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: phykit
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- Version: 2.0.1
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+ Version: 2.0.2
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  Home-page: https://github.com/jlsteenwyk/phykit
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  Author: Jacob L. Steenwyk
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  Author-email: jlsteenwyk@gmail.com
@@ -18,6 +18,14 @@ Requires-Dist: numpy>=1.24.0
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  Requires-Dist: scipy>=1.11.3
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  Requires-Dist: scikit-learn>=1.4.2
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  Requires-Dist: cython
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: license-file
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+ Dynamic: requires-dist
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  <p align="center">
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  <a href="https://github.com/jlsteenwyk/phykit">
@@ -40,9 +48,8 @@ Requires-Dist: cython
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  <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
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  <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
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  </a>
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- <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
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- <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
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- alt="follow on Twitter">
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+ <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
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+ <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
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  </a>
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  <br />
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  <a href="https://pepy.tech/badge/phykit">
phykit-2.0.1/phykit/version.py DELETED
@@ -1 +0,0 @@
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- __version__ = "2.0.1"
{phykit-2.0.1 → phykit-2.0.2}/LICENSE.md RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/phykit/__init__.py RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/phykit/__main__.py RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/phykit/helpers/files.py RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/phykit/phykit.py RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/phykit/services/base.py RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/setup.cfg RENAMED
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{phykit-2.0.1 → phykit-2.0.2}/setup.py RENAMED
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