OpenCloning / OpenCloning/OpenCloning_backend

Should this type of insertion assemble be allowed?

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question
Dominant language
Python
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Forks
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Avg merge
14m
Merged PRs (30d)
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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

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