Metadata-Version: 2.1
Name: exoclasma-note
Version: 0.9.0
Summary: Exo-C Data Quality Check, Mapping, and Variant Calling, part of ExoClasma Suite
Project-URL: Homepage, https://github.com/regnveig/exoclasma-note
Project-URL: Bug Tracker, https://github.com/regnveig/exoclasma-note/issues
Author-email: Emil Viesná <regnveig@yandex.ru>, Minja Fishman <minja-f@yandex.ru>
License-Expression: GPL-3.0-or-later
License-File: LICENSE
Keywords: annotation,bioinformatics,variant
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Requires-Dist: numpy
Requires-Dist: pandarallel
Requires-Dist: pandas
Requires-Dist: pytabix
Description-Content-Type: text/markdown

# exoclasma-note

Annotation of genomic variants.

## Dependencies

Perl:

```bash
sudo apt install perl
```

Annovar:

```bash
GENOME="hg19" # hg38 if you prefer
curl --output annovar.latest.tar.gz www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xzf annovar.latest.tar.gz
cd annovar
for database in refGene knownGene ensGene dbnsfp35c dbscsnv11 intervar_20180118 gnomad211_genome gene4denovo201907 kaviar_20150923 hrcr1 abraom 1000g2015aug gme esp6500siv2_all avsnp150 clinvar_20200316 regsnpintron revel gwava;
do {
	perl annotate_variation.pl -downdb -buildver ${GENOME} -webfrom annovar ${database} humandb/
} done
cd ..
rm annovar.latest.tar.gz
```

## Install

```bash
sudo python3 -m pip install exoclasma-note
```

## Usage

```bash
exoclasma-note -u ${unit_json} -a ${annovar_folder} -g ${genome} [--nofilter]
```

* `unit_json`: Unit JSON file which was created by exoclasma-pipe
* `annovar_folder`: Path to ANNOVAR folder where perl scripts are located
* `genome`: Genome assembly which use ANNOVAR (i.e., hg19, hg38, etc.)
