OpenCloning / OpenCloning/OpenCloning_backend
Should this type of insertion assemble be allowed?
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question
- Dominant language
- Python
- Stars
- 8
- Forks
- 11
- Avg merge
- 14m
- Merged PRs (30d)
- 5
Description
from opencloning.assembly2 import Assembly, assembly2str, assemble
from pydna.dseqrecord import Dseqrecord
template = Dseqrecord('cccgaggggaatcgaa')
insert = Dseqrecord('ggggaatcAcccgag')
asm = Assembly((template, insert), limit=5, use_all_fragments=True)
for a in asm.get_insertion_assemblies():
if a[0][0] == 1:
print(assembly2str(a))
prod = assemble(asm.fragments, a, is_insertion=True)
print(prod.seq)
print()
prints
('1[5:13]:2[0:8]', '2[9:15]:1[0:6]')
cccgaggggaatcAcccgaggggaatcgaa
This is the assembly:
1 cccgaggggaatcgaa
2 Acccgagggggaatc
cccgaggggaatcgaa 1[5:13]
||||||||
ggggaatcAcccgag 2[0:8]
ggggaatcAcccgag 2[9:15]
||||||
cccgaggggaatcgaa 1[0:6]
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Research direction
Run the provided Python example and trace the behavior through Assembly.get_insertion_assemblies and assemble with is_insertion=True. Determine the expected rule for this assembly shape; done means the observed result follows an agreed, documented behavior and has regression coverage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend, bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100