phykit 2.0.1__tar.gz → 2.0.3__tar.gz

{phykit-2.0.1 → phykit-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.0.1
+Version: 2.0.3
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -13,11 +13,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: biopython>=1.82
-Requires-Dist: numpy>=1.24.0
-Requires-Dist: scipy>=1.11.3
-Requires-Dist: scikit-learn>=1.4.2
-Requires-Dist: cython
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">
@@ -40,9 +35,8 @@ Requires-Dist: cython
         <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
             <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
         </a>
-        <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
-            <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
-                alt="follow on Twitter">
+        <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
+          <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
         </a>
         <br />
         <a href="https://pepy.tech/badge/phykit">

{phykit-2.0.1 → phykit-2.0.3}/README.md

@@ -19,9 +19,8 @@
         <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
             <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
         </a>
-        <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
-            <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
-                alt="follow on Twitter">
+        <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
+          <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
         </a>
         <br />
         <a href="https://pepy.tech/badge/phykit">

{phykit-2.0.1 → phykit-2.0.3}/phykit/services/alignment/dna_threader.py

@@ -49,12 +49,36 @@ class DNAThreader(Alignment):
         # triplicate each amino acid
         return ''.join(c * 3 for c in p_seq)
 
-    def normalize_n_seq(self, n_seq: Seq, normalized_p_seq: str) -> str:
-        # insert gaps at corresponding positions in the nucleotide sequence based on the protein sequence
-        normalized_n_seq = list(n_seq)
-        for idx, c in enumerate(normalized_p_seq):
-            if c in "-?*Xx":
-                normalized_n_seq.insert(idx, "-")
+    def normalize_n_seq(self, n_seq: Seq, p_seq: Seq) -> str:
+        # Remove gaps and special characters from protein sequence to get actual amino acids
+        ungapped_p_seq = ''.join(aa for aa in str(p_seq) if aa not in "-?*Xx")
+        
+        # Verify the nucleotide sequence matches the ungapped protein
+        expected_nt_length = len(ungapped_p_seq) * 3
+        if len(n_seq) < expected_nt_length:
+            # If nucleotide sequence is shorter, we'll handle it gracefully
+            # by padding with gaps when we run out of codons
+            pass
+        
+        # Create codons from nucleotide sequence
+        codons = [str(n_seq[i:i+3]) for i in range(0, len(n_seq), 3)]
+        
+        # Map back to gapped alignment - this creates the tripled version
+        normalized_n_seq = []
+        codon_idx = 0
+        
+        for aa in p_seq:
+            if aa in "-?*Xx":
+                # For gaps/special chars, add three gap characters
+                normalized_n_seq.append("---")
+            else:
+                # For actual amino acids, add the corresponding codon
+                if codon_idx < len(codons):
+                    normalized_n_seq.append(codons[codon_idx])
+                    codon_idx += 1
+                else:
+                    normalized_n_seq.append("---")  # fallback in case of misalignment
+        
         return ''.join(normalized_n_seq)
 
     def thread(self, prot_records) -> Dict[str, str]:
@@ -75,7 +99,7 @@ class DNAThreader(Alignment):
                 n_seq = nucl_records[gene_id].seq
 
                 normalized_p_seq = self.normalize_p_seq(p_seq)
-                normalized_n_seq = self.normalize_n_seq(n_seq, normalized_p_seq)
+                normalized_n_seq = self.normalize_n_seq(n_seq, p_seq)
 
                 sequence = [
                     normalized_n_seq[idx] if c not in "-?*Xx" and keep_mask[idx] else "-"

phykit-2.0.3/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.0.3"

{phykit-2.0.1 → phykit-2.0.3}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.0.1
+Version: 2.0.3
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -13,11 +13,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: biopython>=1.82
-Requires-Dist: numpy>=1.24.0
-Requires-Dist: scipy>=1.11.3
-Requires-Dist: scikit-learn>=1.4.2
-Requires-Dist: cython
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">
@@ -40,9 +35,8 @@ Requires-Dist: cython
         <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
             <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
         </a>
-        <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
-            <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
-                alt="follow on Twitter">
+        <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
+          <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
         </a>
         <br />
         <a href="https://pepy.tech/badge/phykit">

phykit-2.0.1/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.0.1"