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April/May analysis refactor #46

Merged
merged 96 commits into from
Jun 1, 2024
Merged

April/May analysis refactor #46

merged 96 commits into from
Jun 1, 2024

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jsstevenson
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jsstevenson and others added 30 commits August 31, 2023 09:07
@jsstevenson
chore: add boilerplate elements and repo skeleton (#1)
afbe4c4
@jsstevenson
feat: add data acquisition methods (#2)
60cde35
@jsstevenson
feat: add initial alignment draft (#3)
161c6be
@jsstevenson
feat: initial transcript selection draft (#4)
7ec36d2
@jsstevenson
feat: initial VRS mapping draft (#5)
1686b95
@jsstevenson
feat: add BLAT output caching/reusing (#6)
d39681e
@jsstevenson
refactor: major edits to VRS mapping and supporting methods (#7)
8c728f5
@jsstevenson
test: fix VRS object test cases (#8)
5f831a2
@jsstevenson
chore: update project metadata (#9)
bf7129b
@jsstevenson
chore: clean up unused code/docstring notes (#10)
0bc6969
@jsstevenson
fix: don't use dnax query for dna target sequences (#11)
cd9573a
@jsstevenson
test: bolster align tests (#12)
3a166a0
@jsstevenson
update TODO
6c703ab
@jsstevenson
test: minor bug-hunting resource rearrangement
092f3c0
@jsstevenson
update TODO
b855c5d
@jsstevenson
test: add transcript selection checks (#13)
b1ccfce
@jsstevenson
cicd: update linting check (#14)
9a2ee61
@jsstevenson
Update TODO.md
a0f79f6
@jsstevenson
Merge pull request #27 from GenomicMedLab/main
2d7d3e0 
See description in README and TODO for progress. Roughly,
- Refactor notebook code into an hopefully-almost-functional end-to-end mapping CLI tool
- Set up minimal packaging metadata
- Add some locally-runnable tests
@jsstevenson
feat: enable configuration of BLAT binary path (#28)
60a7191
@jarbesfeld
Initial refactor for score set breakdown and mapping analysis notebooks
c52f03f
@jarbesfeld
Work in progress, refactor part 3
a8fe91f
@jarbesfeld
Fix hgvs strings
8fcdc5e
@jarbesfeld
Add latest changes
82d14e5
@jarbesfeld
Latest changes
355bb85
@jsstevenson
Add initial VRS 1.3 transform WIP
83cf112
@jarbesfeld
Fix 1.3, VA digest differs
2ecdba8
@jsstevenson
Add initial vrs mapping test
3e3ac34
@jarbesfeld
Add draft converter to VRS 1.x
0ef451c
@jarbesfeld
Morning changes
5180d96
jsstevenson and others added 27 commits May 3, 2024 20:51
@jsstevenson
chore: consolidate annotation methods
00a719a
@jsstevenson
fix: use correct import path
dca627c
@jsstevenson
build: use latest VRS-Python version
39365b3
@jsstevenson
fix: format score as string (unfortunately)
f00156f
@jsstevenson
test: mock vrs 2a6 derive_refget_accession method
6f91b42
@jsstevenson
fix: ensure translator has access to derive_refget_accession
cf143a9
@jsstevenson
refactor: use get_sequence() for sequence fetching
63d9b30
@jsstevenson
chore: remove old type annotation
b43f33c
@jsstevenson
fix: handle hgvs translator complaints about c.
f926bf1
@jsstevenson
test: Add UTA mocks (not working yet
8dfa0a5
@jsstevenson
feat: provide custom mapping save path
5430b93
@jsstevenson
cicd: update tests
93a751e
@jsstevenson
test: move seqrepo mock to shared location
a17034b
@jsstevenson
build: remove 3.8/3.9 classifiers
92e3e3b
@jsstevenson
cicd: don't test before 3.10
090fca0
@jsstevenson
Merge pull request #31 from ave-dcd/analysis_refactor_changes
45de498
@jsstevenson
build: require >=3.10 (#32)
0d2bb51
@jsstevenson
test: reorganize + remove VRS tests from CI (#34)
1a4f7f0
@jsstevenson
feat!: rename VRS 1.3 class (#33)
d872b08
@jsstevenson
docs: update READMEs (#35)
4e68961
@jsstevenson
feat: support ?/Xaa variants (#39)
903f931
@jarbesfeld
Add count of genes
0d54e0c
@jarbesfeld
Edit gene count to reflect S505N MPL target
b912ecb
@jarbesfeld
Change wording for last cell in score set breakdown
d42d45f
@jarbesfeld
Add edge case for hYAP65 in score set breakdown
e621617
@jsstevenson
feat: refactor annotate and VRS_map modules (#41)
76acc91
@jsstevenson
feat: additional analysis refactoring (#47)
67cdf4f
@jsstevenson jsstevenson changed the title Analysis refactor April/May analysis refactor Jun 1, 2024
@jsstevenson jsstevenson merged commit d00598d into main Jun 1, 2024
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@jsstevenson jsstevenson deleted the analysis_refactor branch June 1, 2024 00:41
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2 participants
@jsstevenson @jarbesfeld