EVADumpFiles

Last commit

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

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/eva/EVADumpFiles.java

Contribute

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