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fix bug when double mutations are enabled. #5

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Merged
odcambc merged 1 commit into from
May 24, 2026
Merged

fix bug when double mutations are enabled. #5

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114 changes: 65 additions & 49 deletions DIMPLE/DIMPLE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,23 @@

logger = logging.getLogger(__name__)


def _aa_number(codon_pos: int, frag_start: int, offset: int, primer_buffer: int) -> int:
"""Convert a codon position inside ``tmpseq`` to a 1-indexed AA number.

``tmpseq`` is sliced from ``gene.seq[frag[0] - offset : ...]``, and ``gene.seq``
already skips the start codon (``core.py`` slices at ``start + 3``). With the
canonical configuration ``gene.seq[primer_buffer]`` is therefore the AA 2
codon, so the ``+ 6`` shift maps ``codon_pos == offset`` (first mutable codon
of a fragment that starts at ``primer_buffer``) onto AA 2.

Used by the substitution and deletion paths to label mutations; also by the
make_double pair-lookup, which extracts the AA number from a mutation name
and indexes into a precomputed ``positions`` list — both must agree.
"""
return (frag_start + codon_pos + 6 - offset - primer_buffer) // 3


# Public API. `DIMPLE/DIMPLE.py` re-exports module-split helpers so existing
# `from DIMPLE.DIMPLE import ...` callers keep working. Listed here so ruff F401
# doesn't strip them as unused.
Expand Down Expand Up @@ -479,15 +496,21 @@ def generate_DMS_fragments(
positions = [tmp_positions[i] for i, x in tmp_mut_positions]
else:
mut_positions = range(offset, offset + frag[1] - frag[0], 3)
# Must use the same formula as the mutation-name AA number below,
# since the make_double pair lookup extracts that number from a
# mutation name and indexes into `positions`. Before 2026-05-23
# this used `+ 3` while names used `+ 6`, raising ValueError on
# the last AA of every fragment.
positions = [
int((frag[0] + x + 3 - offset - pool.config.primer_buffer) / 3)
_aa_number(x, frag[0], offset, pool.config.primer_buffer)
for x in mut_positions
]
### Deep Mutational Scanning
if dms:
mutations = {}
for i in mut_positions:
wt_codon = tmpseq[i : i + 3].upper()
aa_pos = _aa_number(i, frag[0], offset, pool.config.primer_buffer)
wt = [
name
for name, codon in gene.SynonymousCodons.items()
Expand Down Expand Up @@ -641,49 +664,20 @@ def generate_DMS_fragments(
f"substitution fragment: {str(xfrag)}"
)
break
mutations[
">"
+ wt[0]
+ str(
int(
(frag[0] + i + 6 - offset - pool.config.primer_buffer)
/ 3
)
)
+ jk
] = mutation[0]
mutations[">" + wt[0] + str(aa_pos) + jk] = mutation[0]
# if there was a synonymous mutation added then add the
# synonymous mutation to the mutation list
if synonymous_mutation:
mutations[
">"
+ wt[0]
+ str(
int(
(
frag[0]
+ i
+ 6
- offset
- pool.config.primer_buffer
)
/ 3
)
)
+ jk
] += (str(synonymous_position) + "_" + synonymous_mutation[0])
mutations[">" + wt[0] + str(aa_pos) + jk] += (
str(synonymous_position) + "_" + synonymous_mutation[0]
)
oligo_id = (
gene.geneid
+ "_DMS-"
+ str(idx + 1)
+ "_"
+ wt[0]
+ str(
int(
(frag[0] + i + 6 - offset - pool.config.primer_buffer)
/ 3
)
)
+ str(aa_pos)
+ jk
)
dms_sequences.append(
Expand All @@ -699,15 +693,10 @@ def generate_DMS_fragments(
mutation_type = "X"
else:
mutation_type = "M"
aa_pos = int(
(frag[0] + i + 6 - offset - pool.config.primer_buffer) / 3
)
name = f"{seq1(wt[0])}{aa_pos}{seq1(jk)}"
gene.designed_variants[oligo_id] = {
"count": 0,
"pos": int(
(frag[0] + i + 6 - offset - pool.config.primer_buffer) / 3
),
"pos": aa_pos,
"mutation_type": mutation_type,
"name": name,
"codon": mutation[0],
Expand Down Expand Up @@ -738,19 +727,46 @@ def generate_DMS_fragments(
+ mutations[combi[1]]
+ tmpseq[pos2 + 3 :]
)
double_name = (
combi[0].strip(">") + "+" + combi[1].strip(">")
)
double_oligo_id = (
gene.geneid + "_DMS-" + str(idx + 1) + "_" + double_name
)
dms_sequences_double.append(
SeqRecord(
xfrag,
id=gene.geneid
+ "_DMS-"
+ str(idx + 1)
+ "_"
+ combi[0].strip(">")
+ "+"
+ combi[1].strip(">"),
id=double_oligo_id,
description="Frag " + fragstart + "-" + fragend,
)
)
# Register the double in designed_variants so the
# shared barcode-assembly loop can stamp the final
# oligo sequence onto it (same shape as the singles
# block at ~line 696 and the DIS registration fix).
gene.designed_variants[double_oligo_id] = {
"count": 0,
"pos": _aa_number(
pos1, frag[0], offset, pool.config.primer_buffer
),
"mutation_type": "MM",
"name": double_name,
"codon": (
str(mutations[combi[0]])
+ "+"
+ str(mutations[combi[1]])
),
"wt_codon": (
str(tmpseq[pos1 : pos1 + 3]).upper()
+ "+"
+ str(tmpseq[pos2 : pos2 + 3]).upper()
),
"mutation": double_name,
"length": 2,
"hgvs": f"p.([{double_name}])",
"fragment": idx + 1,
"xfrag": xfrag,
}
# record mutation for analysis with NGS
# TODO: Don't append.
with open(
Expand Down Expand Up @@ -865,7 +881,7 @@ def generate_DMS_fragments(
# binding region
for i in range(offset - 3, offset + frag[1] - frag[0] - 3, 3):
# Calculate the amino acid position too
pos = int((frag[0] + i + 6 - offset - pool.config.primer_buffer) / 3)
pos = _aa_number(i, frag[0], offset, pool.config.primer_buffer)
# List of wt codons for each position in the range of deletion lengths
wt_codons = [
tmpseq[i + j : i + j + 3].upper() for j in range(0, max(delete), 3)
Expand Down
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