Metadata-Version: 2.1
Name: atlas-metadata-validator
Version: 1.0.0
Summary: A MAGE-TAB validator for Expression Atlas and Single Cell Expression Atlas
Home-page: https://github.com/ebi-gene-expression-group/atlas-metadata-validator
Author: Anja Füllgrabe
Author-email: anjaf@ebi.ac.uk
License: Apache Software License
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: requests (>=2.20.1)

# Expression Atlas metadata validator

This is a python module to parse a set of MAGE-TAB files and check for compatibility with the Expression Atlas and Single Cell Expression Atlas analysis pipelines. The main validation script automatically detects the experiment type from the MAGE-TAB and runs the respective tests. Currently general checks (for bulk and single-cell experiment) as well as Single Cell Expression Atlas specific checks are supported. 

## Requirements

Python 3.6 and requests (tested with version 2.20.1)


## Install

Install with pip:
```
pip install atlas-metadata-validator
```

## Single-cell MAGE-TAB validator

A MAGE-TAB pre-validation module for running checks that guarantee the experiment can be processed for [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home). The checks are mainly covering the pre-validation by https://github.com/ebi-gene-expression-group/scxa-control-workflow/blob/master/bin/sdrfToNfConf.R in order to guarantee correct processing. It reads metadata directly from the MAGE-TAB and generates a log file in the directory of the IDF file.

The checks can be invoked using the atlas_validation script with an IDF file path as input:
```
atlas_validation.py path/to/test.idf.txt 
```

### Options
- The SDRF file is expected in the same directory as the IDF file. If this is not the case, the location of the SDRF and other data files can be specified with `-d PATH_TO_DATA` option.
- The script guesses the experiment type (sequencing, microarray or single-cell) from the MAGE-TAB. If this was unsuccessful the experiment type can be set by specifying the respective argument `-seq`, `-ma` or `-sc`. 
- The data file and URI checks may take long time. Hence there is an option to skip these checks with `-x`.
- Verbose logging can be activated with `-v`.


