OpenCloning / OpenCloning/OpenCloning_backend
assembly edge case not supported since pydna v5.5.14
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- Dominant language
- Python
- Stars
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- Forks
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- Avg merge
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- Merged PRs (30d)
- 5
Description
homology = 'ATGCAAACAGTAATGATGGATGACATTCAAAGCACTGATT'
template = Dseqrecord(f'aaaaaa{homology}aattggaa{homology}tttttttt', circular=False)
insert = Dseqrecord(f'{homology}acaa{homology}', circular=False)
json_template = format_sequence_genbank(template)
json_template.id = 1
json_insert = format_sequence_genbank(insert)
json_insert.id = 2
source = HomologousRecombinationSource(id=0)
data = {'source': source.model_dump(), 'sequences': [json_template.model_dump(), json_insert.model_dump()]}
response = client.post('/homologous_recombination', json=data)
self.assertEqual(response.status_code, 200)
payload = response.json()
sequences = [read_dsrecord_from_json(TextFileSequence.model_validate(s)) for s in payload['sequences']]
self.assertEqual(len(sequences), 3) # This gives 2 now
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the POST to /homologous_recombination with the provided template and insert sequences. Trace the assembly path from that entry point and use the expected three returned sequences, rather than two, as the completion check.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100