From 7c4eedea5351b41919ab7d9532916f586af0fbd8 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 22 Sep 2023 11:29:36 -0700
Subject: [PATCH] factor out reading of hbx2 orfs coordinates

---
 intact/intact.py     | 19 ++++++++++++-------
 util/expected_orf.py |  6 +-----
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/intact/intact.py b/intact/intact.py
index 485586e..761fd8d 100644
--- a/intact/intact.py
+++ b/intact/intact.py
@@ -643,6 +643,15 @@ def strip_sequence_dashes(seq):
         Seq.Seq(str(seq.seq).replace("-","").replace("\n", "")),
         id = seq.id, name = seq.name)
 
+def read_hxb2_orfs(aligned_subtype, orfs):
+    for (name, start, end, delta) in orfs:
+        vpr_defective_insertion_pos = 5771
+        start = start - 1 # Decrement is needed because the original "start" is 1-based.
+        start = start if start < vpr_defective_insertion_pos else start - 1
+        end = end if end < vpr_defective_insertion_pos else end - 1
+
+        yield ExpectedORF.subtyped(aligned_subtype, name, start, end, delta)
+
 def intact( working_dir,
             input_file,
             subtype,
@@ -724,13 +733,9 @@ def analyse_single_sequence(holistic, sequence, blast_rows):
             sequence = aligned_sequence.this
 
         # convert ORF positions to appropriate subtype
-        forward_orfs, reverse_orfs, small_orfs = [
-        [
-            ExpectedORF.subtyped(aligned_subtype, n, s, e, delta) \
-            for (n, s, e, delta) in orfs
-        ] \
-        for orfs in [hxb2_forward_orfs, hxb2_reverse_orfs, hxb2_small_orfs]
-        ]
+        forward_orfs, reverse_orfs, small_orfs = \
+            [list(read_hxb2_orfs(aligned_subtype, orfs)) \
+             for orfs in [hxb2_forward_orfs, hxb2_reverse_orfs, hxb2_small_orfs]]
 
         holistic.orfs_start = min(forward_orfs, key=lambda e: e.start).start
         holistic.orfs_end = max(forward_orfs, key=lambda e: e.end).end
diff --git a/util/expected_orf.py b/util/expected_orf.py
index ac76de1..17cb00a 100644
--- a/util/expected_orf.py
+++ b/util/expected_orf.py
@@ -17,11 +17,7 @@ class ExpectedORF:
 
     @staticmethod
     def subtyped(aligned_sequence, name, start, end, deletion_tolerence):
-        vpr_defective_insertion_pos = 5772
-        start = start if start < vpr_defective_insertion_pos else start - 1
-        end = end if end < vpr_defective_insertion_pos else end - 1
-
-        start_s = ReferenceIndex(start - 1).mapto(aligned_sequence) # decrement is needed because original "start" is 1-based.
+        start_s = ReferenceIndex(start).mapto(aligned_sequence)
         end_s = ReferenceIndex(end).mapto(aligned_sequence)
 
         nucleotides = str(aligned_sequence.this.seq[start_s:end_s])