Metadata-Version: 2.1
Name: anvage
Version: 0.1.0
Summary: toolkit to process routine operation on gff3, vcf and fasta files
Home-page: https://github.com/Grelot/anvage
Author: Pierre-Edouard GUERIN
Author-email: pierre-edouard.guerin@cefe.cnrs.fr
License: MIT
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: argparse
Requires-Dist: numpy
Requires-Dist: biopython
Requires-Dist: bcbio-gff
Requires-Dist: pyfaidx
Requires-Dist: gffutils
Requires-Dist: PyVCF

# anvage
ANnotation Variants GEnome is a toolkit software to perform frequent processing on VCF, GFF3 and FASTA genome



# usage


```
anvage synonymous --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--annotation tests/data/genome.gff3 \
--output_prefix res
```


```
anvage flank --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--windowsSize 25 \
--output_prefix res
```


https://github.com/laurabenestan/BLAST/blob/master/flanking_sequence.py

