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Fix read_dsrecord_from_json, which was not keeping names #414

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Merged
manulera merged 1 commit into from
Mar 6, 2026
Merged

Fix read_dsrecord_from_json, which was not keeping names #414

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13 changes: 4 additions & 9 deletions src/opencloning/dna_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,19 +54,14 @@ def format_sequence_genbank(seq: Dseqrecord, seq_name: str = None) -> TextFileSe
def read_dsrecord_from_json(seq: TextFileSequence) -> Dseqrecord:
with io.StringIO(seq.file_content) as handle:
try:
initial_dseqrecord: Dseqrecord = custom_file_parser(handle, 'genbank')[0]
out_dseq_record: Dseqrecord = custom_file_parser(handle, 'genbank')[0]
except ValueError as e:
raise HTTPException(
422, f'The file for sequence with id {seq.id} is not in a valid genbank format: {e}'
) from e
if seq.overhang_watson_3prime == 0 and seq.overhang_crick_3prime == 0:
out_dseq_record = initial_dseqrecord
else:
out_dseq_record = Dseqrecord(
Dseq.from_full_sequence_and_overhangs(
str(initial_dseqrecord.seq), seq.overhang_crick_3prime, seq.overhang_watson_3prime
),
features=initial_dseqrecord.features,
if seq.overhang_watson_3prime != 0 or seq.overhang_crick_3prime != 0:
out_dseq_record.seq = Dseq.from_full_sequence_and_overhangs(
str(out_dseq_record.seq), seq.overhang_crick_3prime, seq.overhang_watson_3prime
)
# We set the id to the integer converted to integer (this is only
# useful for assemblies)
Expand Down