Version 2.0 by JoshLoecker · Pull Request #252 · HelikarLab/COMO

JoshLoecker · 2026-03-06T19:46:42Z

This is a massive pull request that contains a huge variety of features, improvements, bug fixes, and changes. While these are too numerous to list, the main components include:

Per-data-type input and output controls
- It is now possible to specify exactly where input and output files should be read from and saved to
- This adds some complexity and verbose-ness to each function, but significantly reduces COMO's strictness for file-level organization
Refactored iMAT integration to fix negative-values being placed in middle-expression bin
Fixed FPKM calculations to be on a per-gene basis instead of per-sample
Use Stouffer's method to integrate z-scores
Better handling of incorrect data from remote APIs (e.g., BioDBNet and MyGene.info)
Added integration with Salmon gene quantification and its TPM calculations
Added and updated type hints on significant portions of public (and most private) APIs for easier understanding of what is needed for input and output files/data
Better error and warning messages, plus better error handling

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Co-authored-by: SarahNakamura <snakamura@unomaha.edu>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

…dicates an incorrect taxon id Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

# Conflicts: # main/como/rnaseq_gen.py # main/como/rnaseq_preprocess.py

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

* fix(fpkm): update imports for zFPKM calculation improvements Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(fpkm): use Salmon quantification instead of STAR quantification Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: fill with integers for faster processing Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove unnecessary async function usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: remove non existant genes from conversion Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: use more explicit (albeit longer) code to create gene_info dataframe object Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: import required modules Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: optional argument for fragment data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: improve handling for single cell data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: generalize data type input Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: move zfpkm calculation to external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use np.bool for boolean array Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow setting negative zFPKM results to 0 Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: simplification to use external zfpkm package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow providing the fragment size filepath (from rnaseq preprocessing) Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): reduce max line length Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): mark unsorted imports as fixable Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): lock pyproject file Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: rename count to quant in testing files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: test new quant information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use quant files instead of strand files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: updated COMO_input files for naiveB to use updated FastqToGeneCounts information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: added Salmon quantification data for naive B Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use `_read_file` function to read data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): remove 1 from expected gene names to fix header Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): use `endswith` instead of `is in` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): Use missing file appropriately Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): Use dependency groups Signed-off-by: Josh Loecker <joshloecker@icloud.com> * revert: use synchronous programming for more deterministic usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

* fix(fpkm): update imports for zFPKM calculation improvements Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(fpkm): use Salmon quantification instead of STAR quantification Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: fill with integers for faster processing Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove unnecessary async function usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: remove non existant genes from conversion Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: use more explicit (albeit longer) code to create gene_info dataframe object Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: import required modules Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: optional argument for fragment data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: improve handling for single cell data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: generalize data type input Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: move zfpkm calculation to external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use np.bool for boolean array Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow setting negative zFPKM results to 0 Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: simplification to use external zfpkm package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow providing the fragment size filepath (from rnaseq preprocessing) Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): reduce max line length Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): mark unsorted imports as fixable Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): lock pyproject file Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: rename count to quant in testing files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: add single cell normalization using scanpy defaults Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: test new quant information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: test new quant information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use quant files instead of strand files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use quant files instead of strand files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: updated COMO_input files for naiveB to use updated FastqToGeneCounts information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: added Salmon quantification data for naive B Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use `_read_file` function to read data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): remove 1 from expected gene names to fix header Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): use `endswith` instead of `is in` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): Use missing file appropriately Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): Use dependency groups Signed-off-by: Josh Loecker <joshloecker@icloud.com> * revert: use synchronous programming for more deterministic usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

* fix(fpkm): update imports for zFPKM calculation improvements Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(fpkm): use Salmon quantification instead of STAR quantification Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: fill with integers for faster processing Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove unnecessary async function usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: remove non existant genes from conversion Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: use more explicit (albeit longer) code to create gene_info dataframe object Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: import required modules Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: optional argument for fragment data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: improve handling for single cell data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: generalize data type input Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: move zfpkm calculation to external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use np.bool for boolean array Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow setting negative zFPKM results to 0 Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: simplification to use external zfpkm package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow providing the fragment size filepath (from rnaseq preprocessing) Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): reduce max line length Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): mark unsorted imports as fixable Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): lock pyproject file Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: rename count to quant in testing files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: add single cell normalization using scanpy defaults Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: test new quant information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: test new quant information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use quant files instead of strand files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use quant files instead of strand files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: updated COMO_input files for naiveB to use updated FastqToGeneCounts information Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: added Salmon quantification data for naive B Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use `_read_file` function to read data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): remove 1 from expected gene names to fix header Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): use `endswith` instead of `is in` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(tests): Use missing file appropriately Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): Use dependency groups Signed-off-by: Josh Loecker <joshloecker@icloud.com> * revert: use synchronous programming for more deterministic usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(type): fix pyrefly type errors Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(type): fix ruff & pyrefly issues Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: rename `_log_and_raise_error` to `log_and_raise_error` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: rename `_read_file` to `read_file` Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

* fix(fpkm): update imports for zFPKM calculation improvements Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(fpkm): use Salmon quantification instead of STAR quantification Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: fill with integers for faster processing Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove unnecessary async function usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: remove non existant genes from conversion Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: use more explicit (albeit longer) code to create gene_info dataframe object Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: import required modules Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: optional argument for fragment data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: improve handling for single cell data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: generalize data type input Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: move zfpkm calculation to external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use np.bool for boolean array Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow setting negative zFPKM results to 0 Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: simplification to use external zfpkm package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow providing the fragment size filepath (from rnaseq preprocessing) Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): reduce max line length Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): mark unsorted imports as fixable Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): lock pyproject file Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove zfpkm related code as it is now an external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * revert: remove local pyproject requirement Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove zfpkm testing files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: force sync lock Signed-off-by: Josh Loecker <joshloecker@icloud.com> * Purge `fast_bioservices` (#246) * feat: use bioservice's `MyGeneInfo` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: convert from fast_bioservices to COMO's built-in pipeline Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: remove fast-bioservices from pyproject Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use bioservices over fast_bioservices Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat(test): added unit tests for identifier conversion pipeline Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

* revert: use `raise <error>` instead of `log_and_raise` function Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove non-existant import --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

…elated tests Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Signed-off-by: Josh Loecker <joshloecker@icloud.com> # Conflicts: # .github/workflows/continuous_integration.yml # main/COMO.ipynb # main/como/create_context_specific_model.py # main/como/rnaseq.py # main/como/rnaseq_gen.py # main/como/rnaseq_preprocess.py # pyproject.toml # uv.lock

JoshLoecker added 30 commits December 2, 2024 15:21

refactor: use union operator

c863c54

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: add new function for converting genomic data

1527f18

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

feat: move algorithm options from create context specific

07d6291

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: use logger instead of print

d5dfdc0

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: remove duplicate import

bf072d7

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

feat: import pipeline components

b5998bf

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: use algorith object not strings

1495fc8

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: collect any csv file under preparation method for context

73f36d7

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting

96bf940

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: convert to string before using string operations

d1e5c3a

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: make directory before writing

991a8c2

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: properly check that items exist before using

c32b32d

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: unravel nested lists

951964c

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: proper import sorting and usage

fdc41a4

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: move algorithm to utils

52a6b1f

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: proper docstrings

500bf91

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting; remove unused variables

6a1262a

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: proper error message

49c5e49

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: proper usage of Algorithm

b775798

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting & linting

82ce985

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting & linting; proper docstrings

52c9436

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: proper usage of enum object; async usage

ca4581a

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: proper docstring; added additional directories

a92059c

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting

a7612d1

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff import formatting

8f5c58e

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: proper docstring usage

b0ab689

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: rename private classes and functions; use loguru

24e40e3

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: remove unused arguments

a7486bd

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

feat: reading h5ad files for single-cell analysis

74c4838

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: do not iterate through unnecessary items; ruff formatting

1cd7414

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

JoshLoecker and others added 27 commits October 2, 2025 12:20

Fix Single Cell Processing (#214)

76ccad4

Fix RNA-seq Processing and Boolean Activity Determination (#227)

1df8f39

Co-authored-by: SarahNakamura <snakamura@unomaha.edu>

Fix imat build (#233)

3fc42df

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

refactor: build a FisherExactTest object for validating tests

9597584

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

feat: added log statement and hint to user that an empty dataframe in…

32d7b80

…dicates an incorrect taxon id Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: do not drop na values; keep as much data as possible

e70980b

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

fix: allow empty genomic values

4a44590

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Cobra Types (#237)

f097305

Fix zFPKM Calculations (#238)

0df0142

Add Core zFPKM Tests (#239)

bbb1187

Merge remote-tracking branch 'origin/develop' into develop

e200897

# Conflicts: # main/como/rnaseq_gen.py # main/como/rnaseq_preprocess.py

chore: remove print statement

ef5f7b3

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Use raise instead of log_and_raise function (#247)

aec97d8

* revert: use `raise <error>` instead of `log_and_raise` function Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove non-existant import --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Update metadata files (#248)

36d1b1c

Remove _log_and_raise_error (#249)

1bd400d

Refactor Pipelines (#251)

407219f

chore: remove unused code

6439d02

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting

a5249ea

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

style: ruff formatting

0a929b6

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

chore: import required modules

cac1c5c

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

refactor: enhance model validation functions and streamline glucose-r…

1b61e4e

…elated tests Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Merge branch 'main' of github.com:HelikarLab/COMO

ed45ea5

JoshLoecker marked this pull request as ready for review March 6, 2026 19:52

JoshLoecker merged commit ff9a09f into main Mar 6, 2026
3 checks passed

JoshLoecker deleted the v2 branch March 6, 2026 19:54

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Version 2.0#252

Version 2.0#252
JoshLoecker merged 1574 commits intomainfrom
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JoshLoecker commented Mar 6, 2026 •

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