check reverse before searching for ORFs

cfe-lab · Sep 22, 2023 · cef7223 · cef7223
1 parent 434179a
commit cef7223
Showing 1 changed file with 16 additions and 16 deletions.
diff --git a/intact/intact.py b/intact/intact.py
@@ -710,6 +710,19 @@ def analyse_single_sequence(holistic, sequence, blast_rows):
         reference = subtype_choices[reference_name]
         aligned_subtype = AlignedSequence(this=reference, reference=st.HXB2())
 
+        forward_aligned_sequence = AlignedSequence(this=sequence, reference=aligned_subtype.this)
+        reverse_aligned_sequence = forward_aligned_sequence.reverse()
+
+        forward_score = forward_aligned_sequence.alignment_score()
+        reverse_score = reverse_aligned_sequence.alignment_score()
+        if forward_score >= reverse_score:
+            aligned_sequence = forward_aligned_sequence
+        else:
+            print("Reversing sequence " + sequence.id + "; forward score "
+                    + str(forward_score) + "; reverse score " + str(reverse_score))
+            aligned_sequence = reverse_aligned_sequence
+            sequence = aligned_sequence.this
+
         # convert ORF positions to appropriate subtype
         forward_orfs, reverse_orfs, small_orfs = [
         [
@@ -719,29 +732,16 @@ def analyse_single_sequence(holistic, sequence, blast_rows):
         for orfs in [hxb2_forward_orfs, hxb2_reverse_orfs, hxb2_small_orfs]
         ]
 
-        # convert PSI locus and RRE locus to appropriate subtype
-        psi_locus = [ReferenceIndex(x).mapto(aligned_subtype) for x in hxb2_psi_locus]
-        rre_locus = [ReferenceIndex(x).mapto(aligned_subtype) for x in hxb2_rre_locus]
-
         holistic.orfs_start = min(forward_orfs, key=lambda e: e.start).start
         holistic.orfs_end = max(forward_orfs, key=lambda e: e.end).end
         clamp = lambda p: max(min(p, holistic.orfs_end), holistic.orfs_start)
         aligned_reference_orfs_length = sum(abs(clamp(x.send + 1) - clamp(x.sstart)) for x in blast_rows)
         blast_matched_orfs_slen = holistic.orfs_end - holistic.orfs_start
         holistic.blast_sseq_orfs_coverage = aligned_reference_orfs_length / blast_matched_orfs_slen
 
-        forward_aligned_sequence = AlignedSequence(this=sequence, reference=aligned_subtype.this)
-        reverse_aligned_sequence = forward_aligned_sequence.reverse()
-
-        forward_score = forward_aligned_sequence.alignment_score()
-        reverse_score = reverse_aligned_sequence.alignment_score()
-        if forward_score >= reverse_score:
-            aligned_sequence = forward_aligned_sequence
-        else:
-            print("Reversing sequence " + sequence.id + "; forward score "
-                    + str(forward_score) + "; reverse score " + str(reverse_score))
-            aligned_sequence = reverse_aligned_sequence
-            sequence = aligned_sequence.this
+        # convert PSI locus and RRE locus to appropriate subtype
+        psi_locus = [ReferenceIndex(x).mapto(aligned_subtype) for x in hxb2_psi_locus]
+        rre_locus = [ReferenceIndex(x).mapto(aligned_subtype) for x in hxb2_rre_locus]
 
         alignment = aligned_sequence.get_alignment()