Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

digestion #157

Open
wants to merge 54 commits into
base: develop
Choose a base branch
from
Open

digestion #157

wants to merge 54 commits into from

Conversation

Gonza10V
Copy link
Contributor

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
View reviewed changes
sbol_utilities/component.py Show resolved Hide resolved
sbol_utilities/component.py Outdated Show resolved Hide resolved
sbol_utilities/component.py Outdated Show resolved Hide resolved
sbol_utilities/component.py Show resolved Hide resolved
sbol_utilities/component.py Outdated Show resolved Hide resolved
sbol_utilities/component.py Outdated Show resolved Hide resolved
sbol_utilities/component.py Outdated Show resolved Hide resolved
sbol_utilities/component.py Show resolved Hide resolved
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
View reviewed changes
Copy link
Contributor

@jakebeal jakebeal left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jakebeal jakebeal jakebeal requested changes

Requested changes must be addressed to merge this pull request.

Assignees

@Gonza10V Gonza10V

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@Gonza10V @jakebeal