From 0655c7db7d89cd42e2da57a8a56c6a06e52708ea Mon Sep 17 00:00:00 2001 From: sauter-roland Date: Mon, 1 Apr 2024 14:14:52 +0200 Subject: [PATCH 1/3] Fixing issues with CLI, adding to README, adding to CLI (#37) * csv separator autodetection * more integration tests via cli * Adding proper help text to arguments * adding Recon3D models and sequence data via Git LFS * additional information on readme * json model support for the CLI * add option to only run fast tests * flipping CLI argument order * simplification, fixing tests --- .gitattributes | 2 + .github/workflows/test.yml | 4 + README.md | 55 +- pyproject.toml | 9 +- src/gemcat/cli.py | 243 +- src/gemcat/io.py | 8 +- src/gemcat/workflows.py | 30 + tests/test.ipynb | 215 + tests/test_cli.py | 134 +- tests/test_io.py | 5 +- tests/test_models/.gitattributes | 3 + tests/test_models/Recon3D.json | 3 + tests/test_models/Recon3D_301.json | 3 + tests/test_models/Recon3D_301.mat | 3 + tests/test_models/Recon3D_301.xml | 3 + tests/test_results/uc.csv | 8400 +++++++++++++++++++++ tests/test_seeds.py | 4 +- tests/test_seq/.gitattributes | 2 + tests/test_seq/hek293_rnaseq.csv | 3 + tests/test_seq/prot_uc_vs_healthy.csv | 159 + tests/test_seq/prot_uc_vs_healthy_gid.csv | 3 + 21 files changed, 9102 insertions(+), 189 deletions(-) create mode 100644 .gitattributes create mode 100644 tests/test.ipynb create mode 100644 tests/test_models/.gitattributes create mode 100644 tests/test_models/Recon3D.json create mode 100644 tests/test_models/Recon3D_301.json create mode 100644 tests/test_models/Recon3D_301.mat create mode 100644 tests/test_models/Recon3D_301.xml create mode 100644 tests/test_results/uc.csv create mode 100644 tests/test_seq/.gitattributes create mode 100644 tests/test_seq/hek293_rnaseq.csv create mode 100644 tests/test_seq/prot_uc_vs_healthy.csv create mode 100644 tests/test_seq/prot_uc_vs_healthy_gid.csv diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..96115a0 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +tests/test_seq/prot_uc_vs_healthy_gid.csv filter=lfs diff=lfs merge=lfs -text +tests/test_models/Recon3D.json filter=lfs diff=lfs merge=lfs -text diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8a41811..b816611 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -33,6 +33,10 @@ jobs: steps: - uses: actions/checkout@v3 + with: + lfs: 'true' + - name: Checkout LFS objects + run: git lfs checkout - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: diff --git a/README.md b/README.md index 0edb458..bc8604e 100644 --- a/README.md +++ b/README.md @@ -19,18 +19,46 @@ Or clone the repository and install GEMCAT from there using: ### Standard workflow from the Command-Line Interface (CLI) -``` gemcat ./expression_file.csv ./model_file.xml -e column_name -a pure -g 1.0 -o result_file.csv``` +Use a single file containing per-gene fold-changes to calculate the resulting differential centralities: +``` gemcat ./expression_file.csv ./model_file.xml -e column_name -o ``` +Make sure the .csv file is either comma- or tab-delimited. +`column_name` is the name of the column in the file containing the fold-change. + +Alternatively, use two files (or one file) with expression values for condition and baseline: +``` gemcat <./condition_file.csv> <./model_file.xml> -e -b <./baseline_file> -c -o ``` + +Currently only models in XML/SBML format are supported in the CLI. +Further models can be used from the Python library. +Support will come to the CLI soon. + +Important points to remember: +Your gene or protein identifiers should be the first column of the expression file. +Make sure the gene or protein identifiers in your expression data file exactly match those in the model. +A results list of all 1.0 is a sure sign of no identifier matching. + +positional arguments: +- expression file path +- model file path + +All parameters: +`-e --expressioncolumn` name of column containing condition expression data +`-b BASELINE, --baseline` file containing baseline expression data +`-c BASELINECOLUMN, --baselinecolumn` name of column containing baseline expression data +`-v VERBOSE, --verbose` enables verbose output +`-o OUTFILE, --outfile` write output to this file +`-l LOGFILE, --logfile` write logs to this file ### Standard workflow in Python using a CobraPy model ``` import gemcat as gc -results = gc.workflows.workflow_standard(cobra_model: cobra.Model, - mapped_genes_baseline: pd.Series, - mapped_genes_comparison: pd.Series, - adjacency = gc.adjacency_transformation.ATPureAdjacency, - ranking = gc.ranking.PagerankNX, - gene_fill = 1.0 - ) +results = gc.workflows.workflow_standard( + cobra_model: cobra.Model, + mapped_genes_baseline: pd.Series, + mapped_genes_comparison: pd.Series, + adjacency = gc.adjacency_transformation.ATPureAdjacency, + ranking = gc.ranking.PagerankNX, + gene_fill = 1.0 +) ``` This will return the changes in centrality relative to the baseline in a Pandas Series. When using fold-changes as the mapped expression, use a vector of all ones as a comparison. @@ -60,3 +88,14 @@ Input and output functions that create GEMCAT models from different sources. Contains common utility functions used throughout the package. ## verification Functions to verify data integrity. + + +## Development +You can run all local tests with `pytest .`. Default behavior is to also run integration tests, which takes time. +You can exclude slow running tests by using `pytest . -m "not slow"`. +These slow running tests are integration tests with "real world data" and will take 10-30s each according to your hardware. + +To run tests, make sure you have [git lfs](https://git-lfs.com/) installed and all the Tests are running. +Make sure to run `isort` and `black` to have properly formatted code. + +The CI pipeline in Github will check with isort, black, and pytest. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index b63b93d..7ffafd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "gemcat" -version = "1.0.1" +version = "1.1.0" description = "A toolbox for gene expression-based prediction of metabolic alterations" keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"] @@ -30,6 +30,7 @@ dev = [ "isort>=5.12.0", "pylint>=2.17.7", "ruff>=0.0.292", + "requests>=2.31.0", ] [tool.setuptools.packages.find] @@ -83,3 +84,9 @@ line-length = 88 # Allow unused variables when underscore-prefixed. dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" target-version = "py312" + +[tool.pytest.ini_options] +markers = [ + "slow: Slow running (usually integration) tests. Run only fast tests with '-m \"not slow\"')", + "serial", +] \ No newline at end of file diff --git a/src/gemcat/cli.py b/src/gemcat/cli.py index 58742ce..d574835 100644 --- a/src/gemcat/cli.py +++ b/src/gemcat/cli.py @@ -5,38 +5,17 @@ """ import argparse +import csv import logging +from copy import deepcopy from pathlib import Path from typing import Any, Optional import cobra from pandas import DataFrame, Series, read_csv -from .adjacency_transformation import AdjacencyTransformation, ATPureAdjacency -from .expression import ( - ExpressionIntegration, - ExpressionMapSingleAverage, - GeometricAndAverageMeans, - read_gpr_strings_from_cobra, -) -from .io import convert_cobra_model, load_sbml_cobra -from .ranking import PagerankNX, Ranking - -ADJACENCIES = { - "pure": ATPureAdjacency, -} -ALLOWED_ADJ = ", ".join(ADJACENCIES.keys()) - -RANKINGS = { - "Pagerank": PagerankNX, -} - -EXPRESSION_INTEGRATIONS = { - "means": GeometricAndAverageMeans, - "average": ExpressionMapSingleAverage, -} - -ALLOWED_RANKINGS = ", ".join(RANKINGS.keys()) +from .io import load_json_cobra, load_sbml_cobra +from .workflows import workflow_standard def not_implemented(whatever: Any): @@ -50,29 +29,43 @@ def not_implemented(whatever: Any): MODELS = { - ".sbml": load_sbml_cobra, - ".xml": load_sbml_cobra, - ".json": not_implemented, - ".csv": not_implemented, - ".mat": not_implemented, + "sbml": load_sbml_cobra, + "xml": load_sbml_cobra, + "json": load_json_cobra, + "csv": not_implemented, + "mat": not_implemented, } -def parse_cobra_model(model_path: str) -> cobra.Model: +def wrong_filetype(any: Any): + raise NotImplementedError(f"Not implemented for {any}") + + +def parse_model(model_path: str) -> cobra.Model: + model_path = Path(model_path) + throw_for_missing_model(model_path) + parsing_fn = MODELS[model_path.suffix[1:]] + return parsing_fn(model_path) + + +def get_delimiter(file_path, bytes=4096): + sniffer = csv.Sniffer() + data = open(file_path, "r").read(bytes) + delimiter = sniffer.sniff(data).delimiter + return delimiter + + +def throw_for_missing_model(model_path: Path): """ - Parse selected cobra model - :param model_path: Path to model file + Throw FileNotFoundError in case there is no model at the given path. + :param model_path: _description_ :type model_path: str - :raises FileNotFoundError: If model file does not exist at path - :return: Loaded cobra model - :rtype: cobra.Model + :raises FileNotFoundError: _description_ """ - model_path = Path(model_path) - if not model_path.exists(): + if not model_path.is_file(): error_str = f"The model file at {model_path} cannot be found." logging.error(error_str) raise FileNotFoundError(error_str) - return cobra.io.read_sbml_model(model_path.as_posix()) def read_expression(expression_file: str) -> DataFrame: @@ -90,14 +83,17 @@ def read_expression(expression_file: str) -> DataFrame: error_str = f"File {expression_file} could not be found" logging.error(error_str) raise FileNotFoundError(error_str) - if file_path.suffix == ".csv": - content = read_csv(file_path, sep=",", index_col=0) - elif file_path.suffix == ".tsv": - content = read_csv(file_path, sep="\t", index_col=0) + if file_path.suffix == ".csv" or file_path.suffix == "tsv": + delimiter = get_delimiter(file_path) + content = read_csv(file_path, sep=delimiter, index_col=0) else: - error_str = f"Unknown file format {file_path.suffix} in file {expression_file}" + error_str = ( + f"Unsupported file format {file_path.suffix} in file {expression_file}" + ) logging.error(error_str) raise ValueError(error_str) + if isinstance(content, Series): + return DataFrame(content) return content @@ -113,84 +109,17 @@ def parse_expression(expression_file: str, col_name: Optional[str]) -> Series: :rtype: Series """ content = read_expression(expression_file) - if not content.shape[1] or (content.shape[1] == 1): - content = content.squeeze() - else: - content = content.loc[:, col_name] - if not isinstance(content, Series): - error_str = """ - Expression file must be in the format of a pandas Series, - mapping a gene column to a value column. - """ - logging.error(error_str) - raise ValueError(error_str) - return content - - -def parse_integration(integration: str) -> ExpressionIntegration: - """ - Choice function for expression integration algorithms - :param integration: Name for expression integration algorithm - :type integration: str - :raises ValueError: In case of invalid name - :return: Selected expression integration algorithm - :rtype: ExpressionIntegration - """ - if integration is None: - return GeometricAndAverageMeans - try: - return EXPRESSION_INTEGRATIONS[integration] - except KeyError as original_err: - error_str = f""" - Expression integration method {integration} does not exist. - Allowed methods: {EXPRESSION_INTEGRATIONS} - """ - logging.error(error_str) - raise ValueError(error_str) from original_err - - -def parse_adjacency(adjacency: Optional[str]) -> AdjacencyTransformation: - """ - Choice function for adjacency calculation algorithms - :param adjacency: Name for adjacency calculation algorithm - :type adjacency: Optional[str] - :raises ValueError: In case of invalid name - :return: Selected adjacency transformation algorithm - :rtype: AdjacencyTransformation - """ - if adjacency is None: - return ATPureAdjacency - try: - return ADJACENCIES[adjacency] - except KeyError as original_err: - error_str = f""" - Adjacency model {adjacency} does not exist. - Allowed models: {ALLOWED_ADJ} - """ - logging.error(error_str) - raise ValueError(error_str) from original_err - - -def parse_ranking(ranking: Optional[str]) -> Ranking: - """ - Choice function for ranking algorithms - :param ranking: Name of the ranking algorithm to use - :type ranking: Optional[str] - :raises ValueError: In case of unknown ranking algorithm name - :return: Ranking algorithm - :rtype: Ranking - """ - if ranking is None: - return PagerankNX - try: - return RANKINGS[ranking] - except KeyError as original_err: - error_str = f""" - {ranking} is not a valid ranking method. - Available methods are: {ALLOWED_RANKINGS} - """ - logging.error(error_str) - raise ValueError(error_str) from original_err + if col_name is None and len(content.columns) > 1: + raise ValueError( + """ + If your expression file contains more than 1 column, + please provide the name of the column with the expression data + to the -e flag of the command. + """ + ) + if col_name is None: + return content.iloc[:, 0] + return content.loc[:, col_name] def get_all_ones(expression: Series) -> Series: @@ -201,7 +130,7 @@ def get_all_ones(expression: Series) -> Series: :return: Identical expression series with all entries set to one :rtype: pd.Series """ - return Series(index=expression.index, data=1.0) + return Series(index=deepcopy(expression.index), data=1.0) def parse_outfile(outfile: Optional[str]) -> Path: @@ -232,19 +161,38 @@ def build_parser() -> argparse.ArgumentParser: prog="gemcat", description="GEMCAT tool for metabolomics predictions", ) - parser.add_argument("expressionfile") - parser.add_argument("modelfile") - - parser.add_argument("-i", "--integration") - parser.add_argument("-e", "--expressioncolumn") - parser.add_argument("-r", "--ranking") - parser.add_argument("-b", "--baseline") - parser.add_argument("-c", "--baselinecolumn") - parser.add_argument("-a", "--adjacency") - parser.add_argument("-g", "--genefill") - parser.add_argument("-v", "--verbose") - parser.add_argument("-o", "--outfile") - parser.add_argument("-l", "--logfile") + + parser.add_argument( + "modelfile", help="Path to model file to use (XML/SBML, JSON format)" + ) + parser.add_argument( + "expressionfile", help="Path to file containing the condition expression data" + ) + + parser.add_argument( + "-e", + "--expressioncolumn", + help="Name of the column containing the condition expression data", + ) + parser.add_argument( + "-b", "--baseline", help="File containing expression data for the baseline" + ) + parser.add_argument( + "-c", + "--baselinecolumn", + help="Name of the column contianing the baseline expression data", + ) + parser.add_argument( + "-g", + "--genefill", + type=float, + help="Value to fill in for missing expression values", + ) + parser.add_argument( + "-v", "--verbose", action="store_true", help="Use for more verbose output" + ) + parser.add_argument("-o", "--outfile", help="Write outputs to the specified file") + parser.add_argument("-l", "--logfile", help="Write logs to the specified file") return parser @@ -278,30 +226,19 @@ def cli_standard(args: argparse.Namespace): """ expression = parse_expression(args.expressionfile, args.expressioncolumn) if args.baseline: - baseline = parse_expression(args.baseline, args.baseline_column) + baseline = parse_expression(args.baseline, args.baselinecolumn) else: print("Empty baseline expression. Defaulting to all ones.") baseline = get_all_ones(expression) try: gene_fill = float(args.genefill) except (TypeError, ValueError): - print("Empty or invalid gene-fill value. Defaulting to 1.0 .") + logging.info("Empty or invalid gene-fill value. Defaulting to 1.0 .") gene_fill = 1.0 - - cobra_model = parse_cobra_model(args.modelfile) - model = convert_cobra_model(cobra_model) - model.adjacency_transformation = parse_adjacency(args.adjacency) - model.ranking = parse_ranking(args.ranking) - gpr, rxn_gene_mapping = read_gpr_strings_from_cobra(cobra_model) - integration = parse_integration(args.integration) - expression_obj = integration(gpr, rxn_gene_mapping, expression, gene_fill=gene_fill) - baseline_obj = integration(gpr, rxn_gene_mapping, baseline, gene_fill=gene_fill) - model.load_expression(expression_obj) - results = model.calculate() - model.load_expression(baseline_obj) - results_baseline = model.calculate() - - return results / results_baseline, parse_outfile(args.outfile) + cobra_model = parse_model(args.modelfile) + return workflow_standard( + cobra_model, baseline, expression, gene_fill + ), parse_outfile(args.outfile) def main(): diff --git a/src/gemcat/io.py b/src/gemcat/io.py index 044fe8d..4a5300b 100644 --- a/src/gemcat/io.py +++ b/src/gemcat/io.py @@ -33,7 +33,7 @@ def convert_cobra_model(cobra_model: cobra.Model) -> Model: return Model(stoich_matrix, metabolites, rev) -def load_json_cobra(json_file: Union[str, Path]) -> Model: +def load_json_cobra(json_file: Union[str, Path]) -> cobra.Model: """ Loads a Pagerank-based Model from a COBRA json file. :param json_file: Path to json model file @@ -45,10 +45,10 @@ def load_json_cobra(json_file: Union[str, Path]) -> Model: json_file = json_file.as_posix() cobra_model = cobra.io.load_json_model(json_file) - return convert_cobra_model(cobra_model) + return cobra_model -def load_sbml_cobra(sbml_file: Union[str, Path]): +def load_sbml_cobra(sbml_file: Union[str, Path]) -> cobra.Model: """ Loads a Pagerank-based Model from a COBRA SBML file. :param sbml_file: Path to json SBML file @@ -60,7 +60,7 @@ def load_sbml_cobra(sbml_file: Union[str, Path]): sbml_file = sbml_file.as_posix() cobra_model = cobra.io.read_sbml_model(sbml_file) - return convert_cobra_model(cobra_model) + return cobra_model def load_csv( diff --git a/src/gemcat/workflows.py b/src/gemcat/workflows.py index 7ae5d14..825a469 100644 --- a/src/gemcat/workflows.py +++ b/src/gemcat/workflows.py @@ -14,6 +14,36 @@ from . import ranking as pr +def workflow_single( + cobra_model: cobra.Model, mapped_genes: pd.Series, gene_fill: float +) -> pd.Series: + """ + Workflow using Expression data integration via simple averaging, + provides only the output from a single expression data set. + :param cobra_model: cobra Model used as a base for modeling + :type cobra_model: cobra.Model + :param mapped_genes: Levels of gene/protein expression values + :type mapped_genes: pd.Series + :param gene_fill: Value to fill empty genes with + :type gene_fill: float + :return: Normalized metabolite scores + :rtype: pd.Series + """ + model = io.convert_cobra_model(cobra_model) + gpr, rxn_gene_mapping = ex.read_gpr_strings_from_cobra(cobra_model) + model.adjacency_transformation = at.ATPureAdjacency() + model.ranking = pr.PagerankNX() + ex_comparison = ex.GeometricAndAverageMeans( + gpr=gpr, + reaction_gene_mapping=rxn_gene_mapping, + data=mapped_genes, + gene_fill=gene_fill, + ) + model.load_expression(ex_comparison) + results = model.calculate() + return results + + def workflow_avg_single( cobra_model: cobra.Model, mapped_genes: pd.Series, diff --git a/tests/test.ipynb b/tests/test.ipynb new file mode 100644 index 0000000..3d10066 --- /dev/null +++ b/tests/test.ipynb @@ -0,0 +1,215 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "import gemcat as gc\n", + "import pandas as pd\n", + "import cobra" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "10fthf5glu[c] 1.009677\n", + "10fthf5glu[l] 1.002655\n", + "10fthf5glu[m] 1.013616\n", + "10fthf6glu[c] 1.003871\n", + "10fthf6glu[l] 1.002531\n", + "Name: 0, dtype: float64" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "expected = pd.read_csv('./test_results/uc.csv', index_col=0).iloc[:, 0]\n", + "expected.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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gene_fill=1.0,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "HC01223[m] -0.029117\n", + "M01268[n] -0.012183\n", + "CE4969[m] -0.012028\n", + "2mp2coa[m] -0.011041\n", + "M01268[c] -0.008817\n", + " ... \n", + "pep[c] 0.004107\n", + "3hmp[c] 0.004133\n", + "3hmp[m] 0.006353\n", + "CE4804[m] 0.017471\n", + "M01268[m] 0.036725\n", + "Length: 8399, dtype: float64" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "(expected - results).sort_values()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "pr", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/tests/test_cli.py b/tests/test_cli.py index 749477f..b9aebf4 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,8 +1,11 @@ from dataclasses import dataclass +from pathlib import Path +from subprocess import run from typing import Optional -from numpy import isclose -from pandas import Series +import pytest +from numpy import allclose, isclose +from pandas import Series, read_csv from gemcat import cli @@ -15,32 +18,125 @@ class MockNamespace: baseline: Optional[str] = None baselinecolumn: Optional[str] = None genefill: Optional[str] = None - ranking: Optional[str] = None - adjacency: Optional[str] = None outfile: Optional[str] = None - integration: Optional[str] = None -args_minimal = MockNamespace( - expressionfile="./tests/test_seq/expression_mini.csv", - expressioncolumn=None, - baseline=None, - baselinecolumn=None, - genefill="1.0", - modelfile="./tests/test_models/mini.xml", - ranking=None, - adjacency=None, - outfile="./temp_outfile.csv", - integration="means", -) +expression_path = Path("./tests/test_seq/") +model_path = Path("./tests/test_models/") +results_path = Path("./tests/test_results/") -def test_cli_workflow(): +def test_cli_mini(): + args_minimal = MockNamespace( + expressionfile=str(expression_path / "expression_mini.csv"), + expressioncolumn=None, + baseline=None, + baselinecolumn=None, + genefill="1.0", + modelfile=str(model_path / "mini.xml"), + outfile="./temp_outfile.csv", + ) result, outfile = cli.cli_standard(args_minimal) - print(result) assert isinstance(result, Series) assert outfile.stem == "temp_outfile" assert outfile.suffix == ".csv" assert isclose(result["A"], 1.0, atol=0.001) assert isclose(result["B"], 0.987, atol=0.001) assert len(result) == 4 + + +@pytest.mark.slow +def test_cli_uc_xml(): + args_uc_xml = MockNamespace( + expressionfile=str(expression_path / "prot_uc_vs_healthy_gid.csv"), + expressioncolumn="foldchange", + baseline=None, + baselinecolumn=None, + genefill="1.0", + modelfile=str(model_path / "Recon3D_301.xml"), + outfile="./temp_outfile.csv", + ) + result, outfile = cli.cli_standard(args_uc_xml) + assert isinstance(result, Series) + assert outfile.stem == "temp_outfile" + assert outfile.suffix == ".csv" + + +@pytest.mark.slow +def test_cli_293_xml(): + args_293_xml = MockNamespace( + expressionfile=str(expression_path / "hek293_rnaseq.csv"), + expressioncolumn="wtHEK293_1", + baseline=str(expression_path / "hek293_rnaseq.csv"), + baselinecolumn="wtHEK293_2", + genefill="1.0", + modelfile=str(model_path / "Recon3D_301.xml"), + outfile="./temp_outfile.csv", + ) + result, outfile = cli.cli_standard(args_293_xml) + assert isinstance(result, Series) + assert len(result) > 1000 + assert outfile.stem == "temp_outfile" + assert outfile.suffix == ".csv" + + +@pytest.mark.slow +def test_cli_paper_uc_ns(): + args = MockNamespace( + expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"), + expressioncolumn="foldchange", + baseline=str(expression_path / "prot_uc_vs_healthy.csv"), + baselinecolumn="base", + genefill=None, + modelfile=str(model_path / "Recon3D.json"), + outfile="./temp_outfile.csv", + ) + result, outfile = cli.cli_standard(args) + assert isinstance(result, Series) + assert len(result) > 1000 + assert outfile.stem == "temp_outfile" + assert outfile.suffix == ".csv" + expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0] + assert allclose(expected.values, result.values, atol=0.3) + + +@pytest.mark.slow +def test_cli_paper_uc_wf(): + args = MockNamespace( + expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"), + expressioncolumn="foldchange", + baseline=str(expression_path / "prot_uc_vs_healthy.csv"), + baselinecolumn="base", + genefill=None, + modelfile=str(model_path / "Recon3D.json"), + outfile="./temp_outfile.csv", + ) + result, _ = cli.cli_standard(args) + assert isinstance(result, Series) + assert len(result) > 1000 + expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0] + assert allclose(expected.values, result.values, atol=0.3) + + +@pytest.mark.slow +def test_cli_paper_uc_term(): + out_file = Path("./temp_outfile.csv") + run( + [ + "gemcat", + str(model_path / "Recon3D.json"), + str(expression_path / "prot_uc_vs_healthy.csv"), + "-e", + "foldchange", + "-o", + str(out_file), + "-g", + "1.0", + ], + shell=False, + ) + received = read_csv(out_file, sep=",", index_col=0).iloc[:, 0] + expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0] + out_file.unlink() + assert allclose(expected.values, received.values, atol=0.3) + # the vast majority of metabolites is well behaved, a few show "larger" but inconsequential deviations diff --git a/tests/test_io.py b/tests/test_io.py index b6dd6c3..ef6b7e1 100644 --- a/tests/test_io.py +++ b/tests/test_io.py @@ -14,13 +14,14 @@ def test_convert_cobra_model(models, S_models): def test_json_io(model_files_json, S_models): model_file = model_files_json["mini"] - model = io.load_json_cobra(model_file) + model = io.convert_cobra_model(io.load_json_cobra(model_file)) assert np.allclose(model.stoichiometric_matrix, S_models["mini"]) def test_sbml_io(model_files_sbml, S_models): model_file = model_files_sbml["mini"] - model = io.load_sbml_cobra(model_file) + cobra_model = io.load_sbml_cobra(model_file) + model = io.convert_cobra_model(cobra_model) assert np.allclose(model.stoichiometric_matrix, S_models["mini"]) diff --git a/tests/test_models/.gitattributes b/tests/test_models/.gitattributes new file mode 100644 index 0000000..ab40300 --- /dev/null +++ b/tests/test_models/.gitattributes @@ -0,0 +1,3 @@ +Recon3D_301.xml filter=lfs diff=lfs merge=lfs -text +Recon3D_301.json filter=lfs diff=lfs merge=lfs -text +Recon3D_301.mat filter=lfs diff=lfs merge=lfs -text diff --git a/tests/test_models/Recon3D.json b/tests/test_models/Recon3D.json new file mode 100644 index 0000000..d1552b5 --- /dev/null +++ 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= pr.io.convert_cobra_model(pr.io.load_sbml_cobra(mini_path)) with pytest.raises(ValueError): model.load_metabolite_seeds(seeds) diff --git a/tests/test_seq/.gitattributes b/tests/test_seq/.gitattributes new file mode 100644 index 0000000..52ca5fd --- /dev/null +++ b/tests/test_seq/.gitattributes @@ -0,0 +1,2 @@ +hek293_rnaseq.csv filter=lfs diff=lfs merge=lfs -text +prot_uc_vs_healthy_gid.csv filter=lfs diff=lfs merge=lfs -text diff --git a/tests/test_seq/hek293_rnaseq.csv b/tests/test_seq/hek293_rnaseq.csv new file mode 100644 index 0000000..381f01f --- /dev/null +++ b/tests/test_seq/hek293_rnaseq.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bfc1bcb34f98f8c32887a578a8de12a825e74180a3a6aaa83b57e32497edecba +size 298392 diff --git a/tests/test_seq/prot_uc_vs_healthy.csv b/tests/test_seq/prot_uc_vs_healthy.csv new file mode 100644 index 0000000..32681e6 --- /dev/null +++ b/tests/test_seq/prot_uc_vs_healthy.csv @@ -0,0 +1,159 @@ +gene 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+7381.1,-0.6326468283544214,4.106312668913687e-05,0.644992,1.0 +8875.1,0.779873234407684,0.0790653937452226,1.71698,1.0 +7453.1,0.8065220405507878,0.0001001922217071,1.74899,1.0 diff --git a/tests/test_seq/prot_uc_vs_healthy_gid.csv b/tests/test_seq/prot_uc_vs_healthy_gid.csv new file mode 100644 index 0000000..9f0aa6a --- /dev/null +++ b/tests/test_seq/prot_uc_vs_healthy_gid.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f9deb8dceaac89f72f85f903de675dc62fad7d3aaa69d0bf57becff0d6ce397b +size 9597 From b8d5382d3b25fd638874753cf5cc831daaad0b6c Mon Sep 17 00:00:00 2001 From: Roland Sauter Date: Mon, 1 Apr 2024 14:54:34 +0200 Subject: [PATCH 2/3] adding .mat file support to CLI --- pyproject.toml | 2 +- src/gemcat/cli.py | 4 ++-- src/gemcat/io.py | 20 +++++++++++------ tests/test_cli.py | 56 ++++++++++++++++++----------------------------- 4 files changed, 37 insertions(+), 45 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7ffafd7..2f2a71c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "gemcat" -version = "1.1.0" +version = "1.2.0" description = "A toolbox for gene expression-based prediction of metabolic alterations" keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"] diff --git a/src/gemcat/cli.py b/src/gemcat/cli.py index d574835..dd3e0d9 100644 --- a/src/gemcat/cli.py +++ b/src/gemcat/cli.py @@ -14,7 +14,7 @@ import cobra from pandas import DataFrame, Series, read_csv -from .io import load_json_cobra, load_sbml_cobra +from .io import load_json_cobra, load_mat_cobra, load_sbml_cobra from .workflows import workflow_standard @@ -33,7 +33,7 @@ def not_implemented(whatever: Any): "xml": load_sbml_cobra, "json": load_json_cobra, "csv": not_implemented, - "mat": not_implemented, + "mat": load_mat_cobra, } diff --git a/src/gemcat/io.py b/src/gemcat/io.py index 4a5300b..2992119 100644 --- a/src/gemcat/io.py +++ b/src/gemcat/io.py @@ -41,10 +41,7 @@ def load_json_cobra(json_file: Union[str, Path]) -> cobra.Model: :return: Model object created from the COBRA model :rtype: Model """ - if isinstance(json_file, Path): - json_file = json_file.as_posix() - cobra_model = cobra.io.load_json_model(json_file) - + cobra_model = cobra.io.load_json_model(str(json_file)) return cobra_model @@ -56,10 +53,19 @@ def load_sbml_cobra(sbml_file: Union[str, Path]) -> cobra.Model: :return: Model object created from the COBRA model :rtype: Model """ - if isinstance(sbml_file, Path): - sbml_file = sbml_file.as_posix() - cobra_model = cobra.io.read_sbml_model(sbml_file) + cobra_model = cobra.io.read_sbml_model(str(sbml_file)) + return cobra_model + +def load_mat_cobra(mat_file: Union[str, Path]) -> cobra.Model: + """ + Loads a Pagerank-based Model from a COBRA SBML file. + :param mat_file: Path to json SBML file + :type mat_file: Union[str, Path] + :return: COBRA model object + :rtype: Model + """ + cobra_model = cobra.io.load_matlab_model(str(mat_file)) return cobra_model diff --git a/tests/test_cli.py b/tests/test_cli.py index b9aebf4..fe2b113 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -81,45 +81,31 @@ def test_cli_293_xml(): @pytest.mark.slow -def test_cli_paper_uc_ns(): - args = MockNamespace( - expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"), - expressioncolumn="foldchange", - baseline=str(expression_path / "prot_uc_vs_healthy.csv"), - baselinecolumn="base", - genefill=None, - modelfile=str(model_path / "Recon3D.json"), - outfile="./temp_outfile.csv", - ) - result, outfile = cli.cli_standard(args) - assert isinstance(result, Series) - assert len(result) > 1000 - assert outfile.stem == "temp_outfile" - assert outfile.suffix == ".csv" - expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0] - assert allclose(expected.values, result.values, atol=0.3) - - -@pytest.mark.slow -def test_cli_paper_uc_wf(): - args = MockNamespace( - expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"), - expressioncolumn="foldchange", - baseline=str(expression_path / "prot_uc_vs_healthy.csv"), - baselinecolumn="base", - genefill=None, - modelfile=str(model_path / "Recon3D.json"), - outfile="./temp_outfile.csv", +def test_cli_293_mat(): + out_file = Path("./temp_outfile.csv") + run( + [ + "gemcat", + str(model_path / "Recon3D_301.mat"), + str(expression_path / "prot_uc_vs_healthy.csv"), + "-e", + "foldchange", + "-o", + str(out_file), + "-g", + "1.0", + ], + shell=False, ) - result, _ = cli.cli_standard(args) - assert isinstance(result, Series) - assert len(result) > 1000 - expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0] - assert allclose(expected.values, result.values, atol=0.3) + assert out_file.is_file() + received = read_csv(out_file, sep=",", index_col=0).iloc[:, 0] + out_file.unlink() + assert len(received > 1000) + assert received.isna().sum() == 0 @pytest.mark.slow -def test_cli_paper_uc_term(): +def test_cli_uc_json(): out_file = Path("./temp_outfile.csv") run( [ From 40576a2db920a3fedd02ae11330cf1c5e4b33dc2 Mon Sep 17 00:00:00 2001 From: sauter-roland Date: Sun, 15 Sep 2024 16:10:28 +0200 Subject: [PATCH 3/3] fix package version pinning (#41) * fix pinning of package versions that wasn't working * upgrade pylint as the old version crashed --- pyproject.toml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2f2a71c..1338a37 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "gemcat" -version = "1.2.0" +version = "1.2.1" description = "A toolbox for gene expression-based prediction of metabolic alterations" keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"] @@ -15,22 +15,22 @@ readme = "README.md" requires-python=">=3.10" dependencies = [ - "numpy>=1.26.2", - "pandas>=2.1.4", - "cobra>=0.29.0", - "networkx>=3.2.1", - "scipy>=1.11.4", - "sympy>=1.12", + "numpy==1.26.*", + "pandas==2.1.*", + "cobra==0.29.*", + "networkx==3.2.*", + "scipy==1.11.*", + "sympy==1.12.*", ] [project.optional-dependencies] dev = [ - "pytest>=7.4.0", - "black>=23.7.0", - "isort>=5.12.0", - "pylint>=2.17.7", - "ruff>=0.0.292", - "requests>=2.31.0", + "pytest==7.4.*", + "black==23.7.*", + "isort==5.12.*", + "pylint==3.1.*", + "ruff==0.0.*", + "requests==2.31.*", ] [tool.setuptools.packages.find]