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[1] Dna exten/itp #313

Merged
merged 22 commits into from
Sep 26, 2023
Merged

[1] Dna exten/itp #313

merged 22 commits into from
Sep 26, 2023

Commits on Aug 14, 2023

  1. add function to generate complementary DNA strand for dsDNA

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  2. add test for function to generate complementary DNA strand for dsDNA

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  3. fix test and add circular test-case

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  4. keep edge attributes

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  5. carry over edge attributes

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  6. add link for 3->5 direction

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  7. fix 3,5 link to only apply in one specific case

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  8. use standard convention for DNA

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  9. add dsDNA test

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  10. implement the proper DNA convention when completing strands from sequ… 

    …ence file; also fix cyclic sequences
    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  11. make max_resid a class variable that gets updated automagically; upda… 

    …te DNA convention
    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  12. fix DNA API in gen_itp

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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  13. add backmap attribute in add_node function

    @fgrunewald
    fgrunewald committed Aug 14, 2023
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Commits on Aug 15, 2023

  1. add circle link

    @fgrunewald
    fgrunewald committed Aug 15, 2023
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  2. add test for unkown DNA residue error

    @fgrunewald
    fgrunewald committed Aug 15, 2023
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  3. fix error message in gen_dna

    @fgrunewald
    fgrunewald committed Aug 15, 2023
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  4. add warning for ig format missing title line

    @fgrunewald
    fgrunewald committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. fix test & iterator

    @fgrunewald
    fgrunewald committed Aug 16, 2023
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  2. fix logging for ig format error & add test

    @fgrunewald
    fgrunewald committed Aug 16, 2023
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  3. remove nodes also from fragment graphs; check missing edges for all m… 

    …olecules
    @fgrunewald
    fgrunewald committed Aug 16, 2023
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Commits on Sep 26, 2023

  1. minor opt 

    Co-authored-by: Jan Stevens <[email protected]>
    @fgrunewald @jan-stevens
    fgrunewald and jan-stevens authored Sep 26, 2023
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  2. minor opt 

    Co-authored-by: Jan Stevens <[email protected]>
    @fgrunewald @jan-stevens
    fgrunewald and jan-stevens authored Sep 26, 2023
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