fix bug of testing

BigDataBiology · Jun 12, 2020 · 9024c4b · 9024c4b
1 parent 6b441c6
commit 9024c4b
Showing 1 changed file with 20 additions and 0 deletions.
diff --git a/gmgc_finder/alignment.py b/gmgc_finder/alignment.py
@@ -37,6 +37,26 @@ def category(query, dna_seq, protein_seq):
 
             return 'EXACT'
 
+        else:
+            try:
+                sw_protein = skbio.alignment.local_pairwise_align_ssw(Protein(protein_query), Protein(protein_target),
+                                                                      substitution_matrix=blosum62, gap_open_penalty=11,
+                                                                      gap_extend_penalty=1)
+            except:
+                sw_protein = skbio.alignment.local_pairwise_align_protein(Protein(protein_query),
+                                                                          Protein(protein_target),
+                                                                          substitution_matrix=blosum62,
+                                                                          gap_open_penalty=11, gap_extend_penalty=1)
+            protein_identity, align_length = extract_sw(sw_protein)
+            protein_coverage = align_length / min(len(protein_query), len(protein_target))
+            if protein_identity >= 0.8 and protein_coverage >= 0.8:
+                return 'SIMILAR'
+
+            if protein_identity >= 0.5 and protein_coverage >= 0.5:
+                return 'MATCH'
+
+            return 'NO MATCH'
+
     else:
         try:
             sw_protein = skbio.alignment.local_pairwise_align_ssw(Protein(protein_query),Protein(protein_target),substitution_matrix = blosum62,gap_open_penalty=11,gap_extend_penalty=1)