Improve interoperability by fully supporting the AIRR standard #241
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
commit d9f62d0 Author: Kelvin <kt16@sanger.ac.uk> Date: Thu Feb 11 11:00:05 2021 +0000 Update _convert_anndata.py commit 44d54dd Author: Kelvin <kt16@sanger.ac.uk> Date: Thu Feb 11 10:46:38 2021 +0000 Update _convert_anndata.py initial dict was placed in the wrong position in the for-loop commit 2f20a34 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 11:45:18 2021 +0000 Update _io.py commit 5509588 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 10:57:13 2021 +0000 Update _io.py commit bf79127 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 10:53:07 2021 +0000 Update _io.py commit 0bcd904 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 10:48:06 2021 +0000 Update _io.py commit 118e040 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 10:47:43 2021 +0000 Update _convert_anndata.py commit 9d6ecf9 Author: Kelvin <kt16@sanger.ac.uk> Date: Wed Feb 10 10:45:42 2021 +0000 Update _io.py commit 9e0fa12 Author: Kelvin <kt16@sanger.ac.uk> Date: Tue Feb 9 13:25:25 2021 +0000 Update _io.py commit 6f9ff87 Author: Kelvin <kt16@sanger.ac.uk> Date: Tue Feb 9 12:44:37 2021 +0000 Update __init__.py commit 4393a51 Author: Kelvin <kt16@sanger.ac.uk> Date: Tue Feb 9 12:44:32 2021 +0000 Update _convert_anndata.py add dandelion conversion wrapper commit e224370 Author: Kelvin <kt16@sanger.ac.uk> Date: Tue Feb 9 12:44:18 2021 +0000 Update _io.py Adjustment to allow for reading from pandas dataframe
grst
commented
Mar 21, 2021
zktuong
added a commit
to zktuong/dandelion
that referenced
this pull request
Mar 22, 2021
I think this will make it compliant with scverse/scirpy#241
4 tasks
grst
commented
Mar 30, 2021
zktuong
added a commit
to zktuong/dandelion
that referenced
this pull request
Mar 30, 2021
rename from_scirpy to be more consistent with scverse/scirpy#241
|
@zktuong, pretty much there now, if you want to give it another try. The remaining changes should be mostly related to updating the documentation. |
zktuong
added a commit
to zktuong/dandelion
that referenced
this pull request
Apr 3, 2021
swap to clone_id scverse/scirpy#241 (comment)
|
Yes the round trip back and forth works cleanly regardless of how the airr table is read and processed in dandelion or scirpy! Will update my notebook once it passes the tests (zktuong/dandelion#60). |
Merge_airr_chains previously didn't work on adatas without IR information, and discarded non-IR obs columns from the right anndata object.
|
documentation update in follow-up PR |
zktuong
added a commit
to zktuong/dandelion
that referenced
this pull request
Apr 20, 2021
swap to clone_id scverse/scirpy#241 (comment)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
See also #132 (comment) and #132 (comment)
(although a hacky one: pickling and base64 encoding)(json serialization) of storing excessive chains in an extra chain. They would not be used by scirpy, but it would make reading AIRR files non-destructive.IR_xxxcolumns to match the AIRR schemaexprparameter is specified #253: Tolerate missing columnsclonotypecolumn toclone_id(how to populate IR_*_clone_id columns? #258)Update data loading tutorial (Replaceadata.concatenatewithanndata.concatin the tutorial #255)Go through entire documentation (API and pages), in particular page about data structure.define_clonotypes#257 (save anndata after define_clonotypes)Closes #253
Closes #258
Closes #255
Closes #242
Closes #215