GRange error is out of the range

[iwangtoknow]

Dear digIS authors,

I encountered an error during a digIS run:

ERROR: GRange: start or end position is out of the range.

This error originates from the following lines in digIS.py:

    self.recs.append(
        RecordDigIS.from_hmmer(
            hsp, sid, dna_range[0], dna_range[1], strand,
            self.genome.name, "chr", self.genome.seq, self.genome.length
        )
    )
    self.recs_attrib.append(RecordDigISAttrib(source_type, hsp))

To diagnose the problem, I wrapped the RecordDigIS.from_hmmer() call with a try/except block:

    try:
        self.recs.append(
            RecordDigIS.from_hmmer(
                hsp, sid, dna_range[0], dna_range[1], strand,
                self.genome.name, "chr", self.genome.seq, self.genome.length
            )
        )
    except Exception as e:
        print("ERROR on HSP:")
        print("  sid =", hsp.sid)
        print("  qid =", hsp.qid)
        print("  sstart, send =", hsp.sstart, hsp.send)
        print("  frame =", frame)
        print("  dna_range =", dna_range)
        print("  genome_length =", self.genome.length)
        print("  ERROR:", e)
        raise

Output from the diagnostic:

ERROR on HSP:
  sid = GenBank_CP138752.1_4
  qid = IS1182
  sstart, send = 1598 1665
  frame = 4
  dna_range = (-1, 202)
  genome_length = 4995
  ERROR: GRange: start or end position is out of the range.

The issue seems to be that dna_range contains an invalid coordinate:

dna_range = (-1, 202)

I can provide additional information if needed.

Thank you!

[iwangtoknow]

Dear digIS authors,

After debugging, I traced the problem to the function transform_range() in scr/common/sequence.py.
The issue is the incorrect offset table used for six-frame to DNA coordinate mapping.

---

def transform_range(start, end, frame, seqlen):
    offset = [0, 1, 2, 2, 1, 0][frame-1]   # ← incorrect reverse-frame offsets
    if frame <= 3:
        start_pos = (start-1)*3 + offset + 1
        end_pos = end*3 + offset
    else:
        start_pos = seqlen - (end*3 + offset) + 1
        end_pos = seqlen - ((start-1)*3 + offset)

    return start_pos, end_pos

This leads to invalid coordinates such as:

dna_range = (-1, 202)

for this HSP:

sid = GenBank_CP138752.1_4
qid = IS1182
sstart, send = 1598, 1665
frame = 4
genome_length = 4995

The negative coordinate comes directly from the incorrect reverse-frame offset values.

---

I think the reverse frames (4, 5, 6) should use the same offsets as forward frames because the reading frames restart on the reverse complement:

• Frame 1 → offset 0
• Frame 2 → offset 1
• Frame 3 → offset 2
• Frame 4 → offset 0
• Frame 5 → offset 1
• Frame 6 → offset 2

The correct table should be:

offset = [0, 1, 2, 0, 1, 2][frame-1]

---

Hope this is correct. Thank you for maintaining digIS!