metameq 2026.1.1__tar.gz

metameq-2026.1.1/.gitattributes

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+metameq/_version.py export-subst

metameq-2026.1.1/.github/workflows/main.yaml

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+name: Continuous integration unit testing and lint
+
+on: [push]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10']
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+
+    - name: Install conda environment
+      run: |
+        conda env create -n metameq -f environment.yml     
+
+    - name: Test with pytest
+      run: |
+        conda activate metameq
+        conda install pytest
+        which python
+        pip install -e . --no-deps
+        pytest
+
+    - name: Lint with flake8
+      run: |
+        conda activate metameq
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

metameq-2026.1.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# mac OS
+.DS_Store
+
+# VS Code
+.vscode/

metameq-2026.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: metameq
+Version: 2026.1.1
+Summary: Qiita-compliant metadata generation and validation tool
+Home-page: https://github.com/AmandaBirmingham/metameq
+Author: Amanda Birmingham
+Author-email: abirmingham@ucsd.edu
+License: BSD-3-Clause
+Requires-Dist: click>=8.0.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: PyYAML>=5.4.0
+Requires-Dist: Cerberus>=1.3.4
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
+
+METAMEQ: Metadata Extension Tool to Annotate Microbiome Experiments for Qiita, a tool for generating and validating Qiita-compliant metadata files.

metameq-2026.1.1/README.md

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+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="assets/metameq_dark.svg">
+  <source media="(prefers-color-scheme: light)" srcset="assets/metameq_light.svg">
+  <img alt="METAMEQ logo" src="assets/metameq_medium.png" width="400">
+</picture>
+
+### Metadata Extension Tool to Annotate Microbiome Experiments for Qiita
+
+A python tool to extend an existing tabular metadata file by inferring and adding 
+the standard annotation columns required for submission to [Qiita](https://qiita.ucsd.edu/) and [EBI](https://www.ebi.ac.uk/).
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Installation](#installation)
+- [Basic Usage](#basic-usage)
+- [API Usage](#api-usage)
+
+## Overview
+
+METAMEQ (pronounced “meta-mek”) is a Python-based tool designed to help researchers effortlessly generate standards-compliant microbiome sample metadata. Many data collection standards require specific metadata columns and controlled vocabulary values, which can be time-consuming to assemble manually. METAMEQ streamlines this process by letting users annotate their existing tabular metadata with just two shorthand columns: `hosttype_shorthand` (e.g., human, mouse, non-saline water, etc) and `sampletype_shorthand` (e.g., skin, saliva, feces, wastewater, etc). Once the annotated file is loaded into METAMEQ, the tool automatically expands these shorthand entries into the full set of standardized metadata fields required by multiple community standards, outputting a ready-to-use, enriched metadata file suitable for submission to Qiita and/or EBI. This helps ensure interoperability, reproducibility, and compliance with data sharing best practices.
+
+## Installation
+
+To install this package, first clone the repository from GitHub:
+
+```
+git clone https://github.com/biocore/metameq.git
+```
+
+Change directory into the new `metameq` folder and create a 
+Python3 Conda environment in which to run the software:
+
+```
+conda env create -n metameq -f environment.yml  
+```
+
+Activate the Conda environment and install the package:
+
+```
+conda activate metameq
+pip install -e .
+```
+
+## Basic Usage
+
+METAMEQ is run from the command line using the `metameq` command: 
+
+```bash
+metameq write-extended-metadata METADATA_FILE CONFIG_FILE NAME_BASE [OPTIONS]
+```
+
+### Required Inputs
+
+1. **METADATA_FILE**: Path to your input metadata file containing sample information
+   - Accepted formats: `.csv`, `.txt`, or `.xlsx`
+   - Must include columns for `sample_name`, `hosttype_shorthand`, and `sampletype_shorthand`
+
+2. **CONFIG_FILE**: Path to your study-specific configuration YAML file
+   - Defines study-specific settings like default values and transformation rules
+   - See `config.yml` for an example configuration
+
+3. **NAME_BASE**: Base name suffix for output files
+   - Used to generate output filenames, which will be <timestamp>_<basename>.<extension> (e.g., "2024-05-16_09-46-19_mymetadata.csv" for the name base "mymetadata")
+
+### Optional Parameters
+
+- `--out_dir`: Output directory for generated files (default: current directory)
+- `--sep`: Separator character for text output files.  If ",", the output will be a `.csv` file, and if "\t" the output will be `.txt` file. "\t" is the default
+- `--suppress_fails_files`: Suppress empty QC and validation error files (default: outputs empty files even when no errors found)
+
+### Example
+
+```bash
+metameq write-extended-metadata my_samples.xlsx config.yml my_study_name --out_dir ./output
+```
+
+This command will:
+- Read sample metadata from `my_samples.xlsx`
+- Apply configurations from `config.yml`
+- Generate extended metadata files with standardized fields based on host and sample types
+- Output validation results and QC reports
+- Save all outputs to the `./output` directory with the suffix `my_study_name`
+
+## API Usage
+
+METAMEQ can also be imported and used as a Python library within your own code. This is useful for integrating metadata extension into custom workflows or pipelines.
+
+### Core Functions
+
+The primary functions for programmatic use are:
+
+- **`write_extended_metadata_from_df`**: Extend metadata from a pandas DataFrame and write results to files
+- **`get_extended_metadata_from_df_and_yaml`**: Extend metadata and return DataFrames without writing to disk
+- **`extract_config_dict`**: Load and extract configuration from YAML files
+
+### Basic API Example
+
+```python
+import pandas as pd
+from metameq import (
+    write_extended_metadata_from_df,
+    extract_config_dict,
+    HOSTTYPE_SHORTHAND_KEY,
+    SAMPLETYPE_SHORTHAND_KEY
+)
+
+# Load your raw metadata into a DataFrame
+raw_metadata_df = pd.read_csv("my_samples.csv")
+
+# Ensure required columns exist
+raw_metadata_df[HOSTTYPE_SHORTHAND_KEY] = "human"
+raw_metadata_df[SAMPLETYPE_SHORTHAND_KEY] = "stool"
+
+# Load configuration
+config_dict = extract_config_dict("config.yml")
+
+# Extend metadata and write output files
+extended_df = write_extended_metadata_from_df(
+    raw_metadata_df,
+    config_dict,
+    out_dir="./output",
+    out_name_base="my_study"
+)
+```
+
+### Advanced: Custom Transformers
+
+You can define custom transformation functions for study-specific data processing:
+
+```python
+from metameq import transform_date_to_formatted_date
+
+def custom_date_transformer(row, source_fields):
+    """Custom function to handle date formatting based on sample type."""
+    if row[HOSTTYPE_SHORTHAND_KEY] == "control":
+        return row["extraction_date"]
+    else:
+        return transform_date_to_formatted_date(row, source_fields)
+
+# Pass custom transformers as a dictionary
+transformers = {
+    "custom_date_transformer": custom_date_transformer
+}
+
+extended_df = write_extended_metadata_from_df(
+    raw_metadata_df,
+    config_dict,
+    out_dir="./output",
+    out_name_base="my_study",
+    study_specific_transformers_dict=transformers
+)
+```
+
+### Available Utility Functions
+
+METAMEQ exports several utility functions for data handling:
+
+- **Metadata merging**: `merge_sample_and_subject_metadata`, `merge_many_to_one_metadata`, `merge_one_to_one_metadata`
+- **File loading**: `load_df_with_best_fit_encoding`
+- **Data transformers**: `transform_input_sex_to_std_sex`, `transform_age_to_life_stage`, `format_a_datetime`
+- **Validation**: `get_qc_failures`, `id_missing_cols`, `find_standard_cols`, `find_nonstandard_cols`
+
+### Key Constants
+
+METAMEQ provides constants for required column names:
+
+- `HOSTTYPE_SHORTHAND_KEY`: Column name for host type classification
+- `SAMPLETYPE_SHORTHAND_KEY`: Column name for sample type classification
+- `SAMPLE_NAME_KEY`: Column name for sample identifiers
+- `HOST_SUBJECT_ID_KEY`: Column name for subject identifiers
+- `QC_NOTE_KEY`: Column name for quality control notes

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metameq-2026.1.1/environment.yml

@@ -0,0 +1,14 @@
+name: metameq
+channels:
+  - defaults
+dependencies:
+# NB: if changing here, also change the setup.py install_requires
+  - python
+  - click
+  - pandas
+  - pip
+  - pyyaml
+  - flake8
+  - pep8
+  - pip:
+    - cerberus

metameq-2026.1.1/metameq/__init__.py

@@ -0,0 +1,42 @@
+from metameq.src.util import HOSTTYPE_SHORTHAND_KEY, SAMPLETYPE_SHORTHAND_KEY, \
+    SAMPLE_TYPE_KEY, QC_NOTE_KEY, LEAVE_BLANK_VAL, DO_NOT_USE_VAL, \
+    NOT_PROVIDED_VAL, HOST_SUBJECT_ID_KEY, SAMPLE_NAME_KEY, \
+    COLLECTION_TIMESTAMP_KEY, METADATA_TRANSFORMERS_KEY, SOURCES_KEY, \
+    FUNCTION_KEY, PRE_TRANSFORMERS_KEY, POST_TRANSFORMERS_KEY, \
+    extract_config_dict, deepcopy_dict, load_df_with_best_fit_encoding
+from metameq.src.metadata_configurator import build_full_flat_config_dict
+from metameq.src.metadata_extender import \
+    write_extended_metadata, write_extended_metadata_from_df, \
+    get_reserved_cols, get_extended_metadata_from_df_and_yaml, \
+    write_metadata_results, id_missing_cols, find_standard_cols, \
+    find_nonstandard_cols, get_qc_failures
+from metameq.src.metadata_merger import merge_sample_and_subject_metadata, \
+    merge_many_to_one_metadata, merge_one_to_one_metadata, \
+    find_common_col_names, find_common_df_cols
+from metameq.src.metadata_transformers import \
+    format_a_datetime, standardize_input_sex, set_life_stage_from_age_yrs, \
+    transform_input_sex_to_std_sex, transform_age_to_life_stage, \
+    transform_date_to_formatted_date
+
+__all__ = ["HOSTTYPE_SHORTHAND_KEY", "SAMPLETYPE_SHORTHAND_KEY",
+           "SAMPLE_TYPE_KEY", "QC_NOTE_KEY", "LEAVE_BLANK_VAL",
+           "DO_NOT_USE_VAL", "NOT_PROVIDED_VAL",
+           "HOST_SUBJECT_ID_KEY", "SAMPLE_NAME_KEY",
+           "COLLECTION_TIMESTAMP_KEY", "METADATA_TRANSFORMERS_KEY",
+           "SOURCES_KEY", "FUNCTION_KEY", "PRE_TRANSFORMERS_KEY",
+           "POST_TRANSFORMERS_KEY",
+           "extract_config_dict", "build_full_flat_config_dict",
+           "deepcopy_dict", "load_df_with_best_fit_encoding",
+           "merge_sample_and_subject_metadata", "merge_many_to_one_metadata",
+           "merge_one_to_one_metadata", "find_common_col_names",
+           "find_common_df_cols",
+           "write_extended_metadata", "get_extended_metadata_from_df_and_yaml",
+           "write_extended_metadata_from_df", "write_metadata_results",
+           "get_reserved_cols", "id_missing_cols", "find_standard_cols",
+           "find_nonstandard_cols", "get_qc_failures",
+           "format_a_datetime", "standardize_input_sex",
+           "set_life_stage_from_age_yrs", "transform_input_sex_to_std_sex",
+           "transform_age_to_life_stage", "transform_date_to_formatted_date"]
+
+from . import _version
+__version__ = _version.get_versions()['version']

metameq-2026.1.1/metameq/_version.py

@@ -0,0 +1,21 @@
+
+# This file was generated by 'versioneer.py' (0.29) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2026-01-28T14:30:42-0800",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "b60757af0c4b7b16d71119971565d9991779f6d2",
+ "version": "2026.01.1"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

metameq-2026.1.1/metameq/config/config.yml

@@ -0,0 +1,3 @@
+"default": "not applicable"
+"leave_requireds_blank": false
+"overwrite_non_nans": false