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Improve interoperability by fully supporting the AIRR standard #241

Merged
merged 56 commits into from
Apr 7, 2021
Merged

Improve interoperability by fully supporting the AIRR standard #241

merged 56 commits into from
Apr 7, 2021

Commits on Mar 17, 2021

  1. Allow missing columns in IrObjects

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    grst committed Mar 17, 2021
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  2. Rename Ir{Chain,Cell} to Airr{Chain,Cell}

    @grst
    grst committed Mar 17, 2021
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Commits on Mar 21, 2021

  1. WIP refactor data conversion

    @grst
    grst committed Mar 21, 2021
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  2. Update read_xxx function to map fields to AIRR

    @grst
    grst committed Mar 21, 2021
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  3. Rename cdr3 to junction_aa and cdr3_nt to junction

    @grst
    grst committed Mar 21, 2021
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  4. Fix import errors

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    grst committed Mar 21, 2021
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  5. Merge dandelion integration (by @zktuong) 

    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
    grst committed Mar 21, 2021
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  6. Remove x_gene to x_call

    @grst
    grst committed Mar 21, 2021
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  7. Fix 10x csv test

    @grst
    grst committed Mar 21, 2021
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  8. Fix 10x json test

    @grst
    grst committed Mar 21, 2021
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  9. Fix test for read_tracer

    @grst
    grst committed Mar 21, 2021
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  10. Fix AIRR and Bracer tests

    @grst
    grst committed Mar 21, 2021
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Commits on Mar 30, 2021

  1. Fix 10x roundtrip conversion

    @grst
    grst committed Mar 30, 2021
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  2. Fix fixture

    @grst
    grst committed Mar 30, 2021
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  3. Special treatment for the umi_count column

    @grst
    grst committed Mar 30, 2021
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  4. Implement dandelion conversion

    @grst
    grst committed Mar 30, 2021
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  5. Infer locus from gene calls when not specified in AIRR file

    @grst
    grst committed Mar 30, 2021
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  6. Remove 'omit col' test

    @grst
    grst committed Mar 30, 2021
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  7. Add 10x test data in form of h5ad files

    @grst
    grst committed Mar 30, 2021
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  8. Speed up _is_na

    @grst
    grst committed Mar 30, 2021
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Commits on Mar 31, 2021

  1. Speedup _is_na and _is_true checks

    @grst
    grst committed Mar 31, 2021
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  2. Handle .upper() in sequence dist functions instead of import

    @grst
    grst committed Mar 31, 2021
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  3. prepare handling of airr fields and cell_attributes

    @grst
    grst committed Mar 31, 2021
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Commits on Apr 1, 2021

  1. Implement and test cell_attributes behaviour in AirrCell.

    @grst
    grst committed Apr 1, 2021
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  2. Update docs and type annotations for AirrCell

    @grst
    grst committed Apr 1, 2021
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  3. Fix IO tests, update testing strategy

    @grst
    grst committed Apr 1, 2021
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  4. model multichain as part of dict

    @grst
    grst committed Apr 1, 2021
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  5. Fix AIRR roundtrip conversion issue

    @grst
    grst committed Apr 1, 2021
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  6. Fix more tests

    @grst
    grst committed Apr 1, 2021
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  7. Rename to/form_ir_objs to to/from_airr_cells

    @grst
    grst committed Apr 1, 2021
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  8. Fix issue with converting AirrCell with no chains

    @grst
    grst committed Apr 1, 2021
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  9. Fix merge_adata

    @grst
    grst committed Apr 1, 2021
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  10. Fix #257

    @grst
    grst committed Apr 1, 2021
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Commits on Apr 2, 2021

  1. Implement "upgrade schema" functionality.

    @grst
    grst committed Apr 2, 2021
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  2. Add upgrade schema to datasets module

    @grst
    grst committed Apr 2, 2021
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  3. Put dandelion dependencies in separate group

    @grst
    grst committed Apr 2, 2021
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  4. Rename default clonotype column from 'clonotype' to 'clone_id'

    @grst
    grst committed Apr 2, 2021
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  5. Regenerate expected workflow test data

    @grst
    grst committed Apr 2, 2021
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  6. Documenting and cleaning up IO module

    @grst
    grst committed Apr 2, 2021
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  7. Install adata check decorator to all functions

    @grst
    grst committed Apr 2, 2021
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  8. Fix that clonotype col hasn't been renamed in upgrade_schema

    @grst
    grst committed Apr 2, 2021
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  9. Merge remote-tracking branch 'origin/master' into airr-compliance

    @grst
    grst committed Apr 2, 2021
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  10. CI workaround

    @grst
    grst committed Apr 2, 2021
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  11. Fix workflow test

    @grst
    grst committed Apr 2, 2021
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Commits on Apr 7, 2021

  1. WIP fix docs

    @grst
    grst committed Apr 7, 2021
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  2. Fix docs

    @grst
    grst committed Apr 7, 2021
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  3. Fix #215

    @grst
    grst committed Apr 7, 2021
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  4. Update tutorial after data structure change

    @grst
    grst committed Apr 7, 2021
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  5. Update IO tutorial

    @grst
    grst committed Apr 7, 2021
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  6. Update conda recipe and pytest

    @grst
    grst committed Apr 7, 2021
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  7. Update docs

    @grst
    grst committed Apr 7, 2021
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  8. Fix merge_airr_chains 

    Merge_airr_chains previously didn't work on adatas without
IR information, and discarded non-IR obs columns
from the right anndata object.
    @grst
    grst committed Apr 7, 2021
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  9. Fix missing HDF5 system library in ubuntu CI

    @grst
    grst committed Apr 7, 2021
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  10. Close #255

    @grst
    grst committed Apr 7, 2021
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  11. Fix #257. 

    Fix issue saving anndata with h5py >= 3.0
    @grst
    grst committed Apr 7, 2021
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  12. Fix github actions workflow file

    @grst
    grst committed Apr 7, 2021
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