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Remove hardcoded paths in proteomics #206

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merged 105 commits into from
Dec 11, 2024
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4ce9d8c
feat: initial work to remove hardcoded filepaths
JoshLoecker Dec 5, 2024
90c43f3
chore(deps): bump astral-sh/setup-uv from 3 to 4
dependabot[bot] Dec 5, 2024
bfcafa3
chore(deps): bump astral-sh/ruff-action from 1 to 2
dependabot[bot] Dec 5, 2024
3e81a3d
refactor: allow formatting of jupyter notebooks
JoshLoecker Dec 7, 2024
476ca84
refactor: rename
JoshLoecker Dec 7, 2024
97160e7
refactor: import required libraries
JoshLoecker Dec 7, 2024
0cacd94
refactor: remove unused arguments dataclass
JoshLoecker Dec 7, 2024
9b45c1d
refactor: remove unused cli argument parsing
JoshLoecker Dec 7, 2024
31f59a7
fix: get correct column name
JoshLoecker Dec 7, 2024
8462ab7
refactor: pythonic approach to merging dataframes
JoshLoecker Dec 7, 2024
caea939
style: variable renaming
JoshLoecker Dec 7, 2024
43e1a2e
style: ruff formatting
JoshLoecker Dec 7, 2024
963d481
✨ feat: added gitmoji
JoshLoecker Dec 7, 2024
c389fd9
♻️ refactor: remove commitizen
JoshLoecker Dec 7, 2024
993b4a8
🎨 style: change variable names
JoshLoecker Dec 7, 2024
c4f53bc
🎨 style: sort dependencies
JoshLoecker Dec 7, 2024
9dd5de6
➕ dep-add: add interactive optional dependencies
JoshLoecker Dec 7, 2024
ba0c445
➕ dep-add: add commitizen and conventional gitmoji
JoshLoecker Dec 7, 2024
c7d0576
♻️ refactor: accept file paths instead of dataframes
JoshLoecker Dec 9, 2024
b18383a
📝 docs: update documentation
JoshLoecker Dec 9, 2024
90a6dac
♻️ refactor: accept integers only for taxon IDs
JoshLoecker Dec 9, 2024
e321c3e
♻️ refactor: pythonic approach to calculating size
JoshLoecker Dec 9, 2024
e54309e
♻️ refactor: accept integer for taxon id
JoshLoecker Dec 9, 2024
6cc638f
♻️ refactor: more concise method of creating matrix
JoshLoecker Dec 9, 2024
a348df7
♻️ refactor: remove command line interface
JoshLoecker Dec 9, 2024
c26e12e
♻️ refactor: define specific input/output file paths
JoshLoecker Dec 9, 2024
8ee3f0c
♻️ refactor: remove unnecessary code
JoshLoecker Dec 9, 2024
6a96017
♻️ refactor: allow processing specific filepaths
JoshLoecker Dec 9, 2024
c74e83f
feat: use commitizen for conventional commits
JoshLoecker Dec 9, 2024
b30a54f
feat: update unit tests for rnaseq_preprocess
JoshLoecker Dec 9, 2024
2d78d0b
feat: allow long lines in jupyter notebook
JoshLoecker Dec 9, 2024
7768e27
style: ruff formatting
JoshLoecker Dec 9, 2024
eeef891
fix: ignore F811
JoshLoecker Dec 9, 2024
9b5325e
fix: duplicate noqa directive
JoshLoecker Dec 9, 2024
3279563
refactor: remove unused testing file
JoshLoecker Dec 9, 2024
f262624
test: update tests based on changes
JoshLoecker Dec 9, 2024
02e0a31
fix: do not use asyncio.gather
JoshLoecker Dec 9, 2024
0422633
Merge pull request #192 from HelikarLab/remove-hardcoded-paths/rnaseq…
JoshLoecker Dec 9, 2024
04b47f3
fix: use proper type
JoshLoecker Dec 9, 2024
ad0e007
refactor: remove dependency on Config
JoshLoecker Dec 9, 2024
c2dce72
style: ruff formatting
JoshLoecker Dec 9, 2024
78fcf66
refactor: require output filepath for CPM
JoshLoecker Dec 9, 2024
f06311f
style: log message for calcualted genes
JoshLoecker Dec 9, 2024
7226e36
Merge branch 'main' into remove-hardcoded-paths/rnaseq
JoshLoecker Dec 9, 2024
82044bd
Merge branch 'develop' into remove-hardcoded-paths/rnaseq
JoshLoecker Dec 9, 2024
012a1d9
Merge pull request #193 from HelikarLab/remove-hardcoded-paths/rnaseq
JoshLoecker Dec 9, 2024
293d337
Merge branch 'main' of github.com:HelikarLab/COMO into develop
JoshLoecker Dec 9, 2024
dc91d72
Merge pull request #190 from HelikarLab/dependabot/github_actions/ast…
JoshLoecker Dec 9, 2024
1e01b34
Merge pull request #189 from HelikarLab/dependabot/github_actions/ast…
JoshLoecker Dec 9, 2024
c7b234f
Merge branch 'develop' of github.com:HelikarLab/COMO into develop
JoshLoecker Dec 9, 2024
355b9df
refactor: remove rnaseq.py
JoshLoecker Dec 9, 2024
a43b20d
refactor: import items from rnaseq.py
JoshLoecker Dec 9, 2024
5675a35
refactor: remove command line usage
JoshLoecker Dec 9, 2024
b5a199c
refactor: add classes for rna processing
JoshLoecker Dec 9, 2024
5a2dd33
feat: added k_over_a calculation
JoshLoecker Dec 9, 2024
fbb2b76
feat: added genefilter function
JoshLoecker Dec 9, 2024
1de1717
refactor: create separate read_counts matrix
JoshLoecker Dec 9, 2024
279f7cc
feat: bring zfpkm_filter from rnaseq.py
JoshLoecker Dec 9, 2024
7e2fe3d
feat: added matrix builder
JoshLoecker Dec 9, 2024
9eaa2ac
feat: added tpm calculation
JoshLoecker Dec 9, 2024
3670016
feat: added fpkm calculation
JoshLoecker Dec 9, 2024
1cd4dbb
feat: added zfpkm transformation and calculation
JoshLoecker Dec 9, 2024
dd8698e
feat: added zfpkm plotting
JoshLoecker Dec 9, 2024
01db1ef
feat: aded calculate z score
JoshLoecker Dec 9, 2024
a47f752
feat: added cpm filtering
JoshLoecker Dec 9, 2024
b6460c2
feat: added tpm quantile filtering
JoshLoecker Dec 9, 2024
e0c98b4
feat: added root filtering logic
JoshLoecker Dec 9, 2024
a4d6f2f
feat: added logic for performing statistical tests
JoshLoecker Dec 9, 2024
e9665bf
feat: create metadata df
JoshLoecker Dec 9, 2024
dc7c1fe
refactor: allow passing specific filepaths
JoshLoecker Dec 9, 2024
f35e09a
refactor: rename variable names for easier reuse
JoshLoecker Dec 9, 2024
fc803bc
style: update log message, more pythonic code
JoshLoecker Dec 10, 2024
8bdddd9
style: variable rename
JoshLoecker Dec 10, 2024
e0d84be
feat: update to match new approach
JoshLoecker Dec 10, 2024
9674459
revert: use mrna instead of polya
JoshLoecker Dec 10, 2024
cde6606
refactor: check files returned
JoshLoecker Dec 10, 2024
b14d3f9
feat: allow specifying specific directories
JoshLoecker Dec 10, 2024
d52b0ee
style: use more descriptive variable names
JoshLoecker Dec 10, 2024
fe1d406
refactor: use early continue
JoshLoecker Dec 10, 2024
8f1d027
style: update warning messages
JoshLoecker Dec 10, 2024
0ef736e
style: rename variables
JoshLoecker Dec 10, 2024
3825aa2
refactor: move filtering technique to types
JoshLoecker Dec 10, 2024
b0fa60e
fix: do not use more cores than necessary
JoshLoecker Dec 10, 2024
911aaaa
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
2bfe760
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
f8ebcbf
Merge branch 'develop' into remove-hardcoded-paths/rnaseq-gen
JoshLoecker Dec 11, 2024
6bd06e1
fix: use parenthesis to validate calculations
JoshLoecker Dec 11, 2024
f24347d
refactor: ignore missing variables for now
JoshLoecker Dec 11, 2024
1956721
chore: ignore complex function
JoshLoecker Dec 11, 2024
179c673
Merge pull request #199 from HelikarLab/remove-hardcoded-paths/rnaseq…
JoshLoecker Dec 11, 2024
65bd2a3
chore: remove unused imports
JoshLoecker Dec 11, 2024
3cc9bec
refactor: remove command line interface
JoshLoecker Dec 11, 2024
0f9bd3a
feat: process input data more pythonically
JoshLoecker Dec 11, 2024
1402016
refactor: do not use hardcoded filepaths
JoshLoecker Dec 11, 2024
450c9e9
chore: ruff formatting
JoshLoecker Dec 11, 2024
01b31df
style: use better variable name & reorganize
JoshLoecker Dec 11, 2024
06e0932
feat: process the provided file paths
JoshLoecker Dec 11, 2024
4baf95a
feat: write to provided filepath
JoshLoecker Dec 11, 2024
9f97001
refactor: remove hardcoded filepaths
JoshLoecker Dec 11, 2024
bfe8d7e
refactor: pythonic approach to processing
JoshLoecker Dec 11, 2024
c401696
fix: arguments to write data
JoshLoecker Dec 11, 2024
870cdb9
Merge pull request #205 from HelikarLab/remove-hardcoded-paths/proteo…
JoshLoecker Dec 11, 2024
93ac383
Merge branch 'main' of github.com:HelikarLab/COMO into remove-hardcod…
JoshLoecker Dec 11, 2024
c7da971
feat: allow specifiying files to process
JoshLoecker Dec 11, 2024
4c381ca
fix: no longer require rna processing type
JoshLoecker Dec 11, 2024
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10 changes: 4 additions & 6 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/opensource-nepal/commitlint
rev: v1.2.0
- repo: https://github.com/commitizen-tools/commitizen
rev: master
hooks:
- id: commitlint
name: Commit Lint
- id: commitizen
stages: [ commit-msg ]
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