exoclasma-note
Annotation of genomic variants.
Dependencies
Perl:
sudo apt install perl
Annovar:
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
sudo python3 -m pip install exoclasma-note
Usage
exoclasma-note -u ${unit_json} -a ${annovar_folder} -g ${genome} [--nofilter]
unit_json: Unit JSON file which was created by exoclasma-pipeannovar_folder: Path to ANNOVAR folder where perl scripts are locatedgenome: Genome assembly which use ANNOVAR (i.e., hg19, hg38, etc.)
1 maintainer
Metadata
1 maintainer
Release files for exoclasma-note 0.9.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| exoclasma_note-0.9.0-py3-none-any.whl | Python 3 | none | any | Details for exoclasma_note-0.9.0-py3-none-any.whl |
Release files / exoclasma_note-0.9.0-py3-none-any.whl
| Download URL | exoclasma_note-0.9.0-py3-none-any.whl |
|---|---|
| Size | 18.2 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
7245a7efaa1504c21a442cad020b4790e87d7a0e5a5c26486cc1b94770e67a23
|
|
BLAKE2b-256 checksum How to use checksums |
6466a951da1537b47ad534fc0d796dc11e85c1665f3fdfccd2a0d6252de93e55
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.4.2 requests/2.22.0 setuptools/45.2.0 requests-toolbelt/0.8.0 tqdm/4.64.0 CPython/3.8.10
|
Security for exoclasma-note 0.9.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
