EVADumpFiles
Dump files locations from European Variation Archive
Usage
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar evadumpfiles [options] Files
Usage: evadumpfiles [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--taxons, --taxon
define one or more taxon filters:syntax 'taxonCode assemblyCode' or
'taxonCode *' or 'taxonCode' .eg: 'cfamiliaris' , 'cfamiliaris * ',
'cfamiliaris 31'. Multiple are comma/semicolon separated. See output of
https://www.ebi.ac.uk/eva/webservices/rest/v1/meta/species/list/ .
Default: []
--version
print version and exit
Keywords
- eva
- ebi
- snp
- variant
Creation Date
20230314
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite evadumpfiles ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example
$ java -jar dist/jvarkit.jar evadumpfiles --taxons 'cfamiliaris 31' 2> /dev/null | verticalize
>>> 2
$1 studyId PRJEB56315
$2 studyName Idiopathic Epilepsy in the Dutch partridge dog
$3 assemblyAccession GCA_000002285.2
$4 assemblyName CanFam3.1
$5 taxonomyCommonName Dog
$6 taxonomyScientificName Canis lupus familiaris
$7 taxonomyId 9615
$8 taxonomyCode cfamiliaris
$9 assemblyCode 31
$10 file https://ftp.ebi.ac.uk/pub/databases/eva/PRJEB56315/variants_pass.vcf.gz
<<< 2
>>> 3
$1 studyId PRJEB56211
$2 studyName Performance of Variant Pathogenicity Prediction Methods
$3 assemblyAccession GCA_000002285.2
$4 assemblyName CanFam3.1
$5 taxonomyCommonName Dog
$6 taxonomyScientificName Canis lupus familiaris
$7 taxonomyId 9615
$8 taxonomyCode cfamiliaris
$9 assemblyCode 31
$10 file https://ftp.ebi.ac.uk/pub/databases/eva/PRJEB56211/VPP_Project_Variants.vcf.gz
<<< 3
>>> 4
$1 studyId PRJEB51024
$2 studyName Longevity of Cane Corso Italiano purebred dogs
$3 assemblyAccession GCA_000002285.2
$4 assemblyName CanFam3.1
$5 taxonomyCommonName Dog
$6 taxonomyScientificName Canis lupus familiaris
$7 taxonomyId 9615
$8 taxonomyCode cfamiliaris
$9 assemblyCode 31
$10 file https://ftp.ebi.ac.uk/pub/databases/eva/PRJEB51024/cane_corso_f.vcf.gz