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digestion #157

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@Gonza10V Gonza10V commented Jul 25, 2022

digestion function

@Gonza10V Gonza10V self-assigned this Jul 25, 2022
@Gonza10V Gonza10V requested a review from jakebeal July 25, 2022 14:54
jakebeal
jakebeal reviewed Jul 25, 2022
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Gonza10V and others added 25 commits July 27, 2022 12:17
@Gonza10V @jakebeal
updating sequence number cheking error message
e26c2c8 
Co-authored-by: Jacob Beal <[email protected]>
@Gonza10V @jakebeal
Update digested_reactant logic
944c0ab 
Co-authored-by: Jacob Beal <[email protected]>
@Gonza10V
updated digestion
9a4e8c5
@Gonza10V
Merge pull request #163 from SynBioDex/develop
9e59f64 
update RDF validation
@Gonza10V
removing -1 from sequence computation on open backbone
c22bfec
@Gonza10V
Merge branch 'gonzalo-internship3' of github.com:SynBioDex/SBOL-utili…
12b7319 
…ties into gonzalo-internship3
@Gonza10V
updating testing with sequence computation
3d7ed6a
@Gonza10V
advances in ligation and is_circular helper function
b954a19
@Gonza10V
advances on ligation process logic
1fa1049
@Gonza10V
advances on components creation
7efbb2c
@Gonza10V
ligation prototype
bbf4138
@Gonza10V
assembly and part in backbone2
0adb6ee
@Gonza10V
functional digestion
b970902
@Gonza10V
updated components and tests
627dba9
@Gonza10V
Merge pull request #1 from Gonza10V/gonzalo-internship3
3d2990d 
Gonzalo internship3
@Gonza10V
Merge branch 'SynBioDex:develop' into develop
44e4bc9
@Gonza10V
Merge pull request #2 from Gonza10V/develop
f92d4af 
updating gonzalo internship3
@Gonza10V
updated version part_in_backbone_from_sbol
baa89ee
@Gonza10V
test in separated routines
9f07fff
@Gonza10V
provide a correct file direction for convert_from_genbank
a212530
@Gonza10V
using paterns in sbol-utilities for directories
599be7e
@Gonza10V
add dir from codebase on test_part_in_backbone_from_sbol_bp011
260b4d1
@Gonza10V
adding objects to the document
8cb7404
@Gonza10V @jakebeal
Update sbol_utilities/component.py
02e71f4 
fixes typo a in length

Co-authored-by: Jacob Beal <[email protected]>
@Gonza10V @jakebeal
Update sbol_utilities/component.py
3d68860 
improves doctring that explain overwrite param

Co-authored-by: Jacob Beal <[email protected]>
Gonza10V and others added 25 commits March 30, 2023 13:20
@Gonza10V
update
a44b8b2
@Gonza10V
Merge branch 'gonzalo-internship3' of github.com:Gonza10V/SBOL-utilit…
734b3fa 
…ies into gonzalo-internship3
@Gonza10V
changes in response to code review 27/03/23
2caea26
@Gonza10V
if identity is not none overwrite the SBOL component
ccf6aba
@Gonza10V
improved test_part_in_backbone_from_sbol_bp011
63d3414
@Gonza10V
asserts with sets
a7c3592
@Gonza10V @jakebeal
Update sbol_utilities/component.py
0717c46 
Co-authored-by: Jacob Beal <[email protected]>
@Gonza10V
adds TODOs
d33c3e5
@Gonza10V
minor changes on comments
5d86cf5
@jakebeal
Merge pull request #192 from Gonza10V/gonzalo-internship3
d0460e5 
SEP055 implementation
@Gonza10V
combinatorial assembly and backbone from sbol
468d94a
@Gonza10V
Merge branch 'SynBioDex:gonzalo-internship3' into gonzalo-internship3
80c813f
@Gonza10V
adding notebook
3d6598f
@Gonza10V
Merge branch 'gonzalo-internship3' of github.com:Gonza10V/SBOL-utilit…
101742f 
…ies into gonzalo-internship3

comit
@Gonza10V
update in engineered region
335c1d9 
starting at 0 rather that at one for order of features
@Gonza10V
appending constraints to er
421a076
@Gonza10V
swapping er features order on constraints
193ec3e
@Gonza10V
now fixing order is optional on er
5ab7e2a
@Gonza10V
fixing order is optional and uses meets intead of preceeds
4408543
@Gonza10V
adding a new document to test linear backbone
408a297 
adding a new document to test linear backbone from SBOL
@Gonza10V
replacing meets for precedes in engineered region
f36b5b1
@Gonza10V
order is fixed by default un enr
5b77186
@Gonza10V
testing now appending constraints
4e0e958
@Gonza10V
Merge pull request #3 from SynBioDex/gonzalo-internship3
db85c64 
testing now appending constraints
@Gonza10V
Merge pull request #233 from Gonza10V/gonzalo-internship3
f9e565c 
BP011
@Gonza10V Gonza10V added the enhancement New feature or request label Mar 27, 2024
jakebeal
jakebeal requested changes Apr 7, 2024
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In addition to the two expected failures due to #231, there is a failing round-trip test. Can you please identify and resolve the issue?

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