Metadata-Version: 2.1
Name: breathpy
Version: 0.9.1
Summary: Breath analysis in python
Home-page: https://github.com/philmaweb/breathpy
Author: Philipp Weber
Author-email: pweber@imada.sdu.dk
License: GPLv3
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: graphviz (>=0.13.2)
Requires-Dist: ipdb
Requires-Dist: matplotlib (>=3.2.1)
Requires-Dist: matplotlib-venn (>=0.11.5)
Requires-Dist: numpy (>=1.18.1)
Requires-Dist: pandas (>=1.0.3)
Requires-Dist: psutil (>=3.4.2)
Requires-Dist: pyopenms (==2.4.0)
Requires-Dist: pywavelets (>=1.1.1)
Requires-Dist: scikit-image (>=0.16.2)
Requires-Dist: scikit-learn (<0.23.0,>=0.22.0)
Requires-Dist: scipy (>=1.4.1)
Requires-Dist: seaborn (>=0.10.0)
Requires-Dist: statannot (>=0.2.3)
Requires-Dist: statsmodels (>=0.11.1)
Requires-Dist: xlrd (>=1.2.0)

[![DOI](https://zenodo.org/badge/267952107.svg)](https://zenodo.org/badge/latestdoi/267952107)

# BreathPy
## A Python Library for Breath Analysis, Preprocessing, Visualization and Classification of Multi-Capillary-Column Ion-Mobility-Spectrometry data

## Installation

`BreathPy` depends on `python >=3.6` and is available through `pip`. Make sure to activate your local virtual environment or use anaconda. To render decision trees we depend on the `graphviz` executable. Either install into your current environment using `pip install breathpy` or create, activate a new anaconda environment "breath" and install `breathpy` and `graphviz`:  
```bash
conda create --name breath python pip graphviz -y
conda activate breath
pip install breathpy
```

If you want to use the tutorial jupyter notebooks - you want to install jupyter `conda install jupyter`.

## Usage MCC-IMS

First prepare the example dataset by creating a subdirectory `data` and then linking the example files there.
```python
from pathlib import Path
from urllib.request import urlretrieve
from zipfile import ZipFile

# download example zip-archive
url = 'https://github.com/philmaweb/BreathAnalysis.github.io/raw/master/data/small_candy_anon.zip'
zip_dst = Path("data/small_candy_anon.zip")
dst_dir = Path("data/small_candy_anon/")
dst_dir.mkdir(parents=True, exist_ok=True)
urlretrieve(url, zip_dst)

# unzip archive into data subdirectory
with ZipFile(zip_dst, "r") as archive_handle:
    archive_handle.extractall(Path(dst_dir))
```   

Then run the example analysis like so:
```python
# import required functions
from breathpy.model.BreathCore import construct_default_parameters, construct_default_processing_evaluation_steps
from breathpy.model.CoreTest import run_start_to_end_pipeline

# define file prefix and default parameters
file_prefix = folder_name = 'small_candy_anon'

# assuming the data directory is in the current directory
plot_parameters, file_parameters = construct_default_parameters(file_prefix, folder_name, make_plots=True)

# create default parameters for preprocessing and evaluation
preprocessing_steps, evaluation_params_dict = construct_default_processing_evaluation_steps()

# call start
run_start_to_end_pipeline(plot_parameters, file_parameters, preprocessing_steps, evaluation_params_dict)
```

For more complete examples see `tutorial/binary_candy.ipynb`, `tutorial/multiclass_mouthwash.ipynb' or 'CoreTest.run_start_to_end_pipeline` and `CoreTest.run_resume_analysis`.
Example data is available at https://github.com/philmaweb/BreathAnalysis.github.io/tree/master/data.

## Usage GC-MS
### Now with experimental support for GC/MS + LC/MS data through pyOpenMS
Download and extract the example datasets into the current data subdirectory:
```bash
wget "https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/raw/master/data_sets/Example_Jul0914_mzXML.zip"
wget "https://github.com/bioinformatics-ca/bioinformatics-ca.github.io/raw/master/data_sets/Example_Jul1114_mzXML.zip"
mkdir -p "data/eoe"
unzip Example_Jul1114_mzXML.zip -d data/eoe/
# overwrite the blank and alkstdt
unzip -o Example_Jul0914_mzXML.zip -d data/eoe/
# download class_labels.csv file
wget -O data/eoe/eoe_class_labels.csv "https://github.com/philmaweb/BreathAnalysis.github.io/raw/master/data/eoe_class_labels.csv"
```

```python
from pathlib import Path
import os
from breathpy.model.BreathCore import construct_default_parameters,construct_default_processing_evaluation_steps
from breathpy.model.ProcessingMethods import GCMSPeakDetectionMethod, PerformanceMeasure
from breathpy.model.GCMSTest import run_gcms_platform_multicore
from breathpy.generate_sample_data import generate_train_test_set_helper

"""
Runs analysis of Eosinophilic Esophagitis (EoE) sample set with 40 samples - gcms measurements
Dataset from https://bioinformaticsdotca.github.io/metabolomics_2018_mod2lab
:param cross_val_num:
:return:
"""
cross_val_num=5
# or use your local path to a dataset here
source_dir = Path(os.getcwd())/"data/eoe"
target_dir = Path(os.getcwd())/"data/eoe_out"

# will delete previous split and rewrite data
train_df, test_df = generate_train_test_set_helper(source_dir, target_dir, cross_val_num=cross_val_num)
train_dir = Path(target_dir)/"train_eoe"

# prepare analysis
set_name = "train_eoe"
make_plots = True

# generate parameters
# if executing from breathpy directory use execution_dir_level='project',
plot_parameters, file_parameters = construct_default_parameters(set_name, set_name, make_plots=make_plots,
                                                                execution_dir_level='project')
preprocessing_params_dict = {GCMSPeakDetectionMethod.ISOTOPEWAVELET: {"hr_data": True}}
_, evaluation_params_dict = construct_default_processing_evaluation_steps(cross_val_num)

run_gcms_platform_multicore(sample_dir=train_dir, preprocessing_params=preprocessing_params_dict, evaluation_parms=evaluation_params_dict)
```
Also see `model/GCMSTest.py` for reference. 

### License
`BreathPy` is licensed under GPLv3, but contains binaries for PEAX, which is a free software for academic use only.
See
> [A modular computational framework for automated peak extraction from ion mobility spectra, 2014, D’Addario *et. al*](https://doi.org/10.1186/1471-2105-15-25)

## Contact
If you run into difficulties using `BreathPy`, please open an issue at our [GitHub](https://github.com/philmaweb/BreathPy) repository. Alternatively you can write an email to [Philipp Weber](mailto:pweber@imada.sdu.dk?subject=[BreathPy]%20BreathPy).


