Enveomics collection

EBIseq2tax.rb

Maps a list of EBI-supported IDs to their corresponding NCBI taxonomy using EBI RESTful API.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.
• Ruby gem nokogiri.

§ Usage

§ Arguments

IDs

 --ids string  Comma-separated list of EBI IDs.

Required unless 'Input file' is passed.

Input file

 --infile in_file  Raw text file containing the list of EBI IDs, one per line.

Required unless 'IDs' is passed.

Database

 --database string  EBI database defining the EBI IDs.

Ranks

 --ranks string  Comma-delimited list of taxonomic ranks to report.

Noheader

 --noheader   Do not includ a header in the output.

Taxids

 --taxids   Return Taxonomy IDs instead of scientific names.

Quiet

 --quiet   Run quietly.