Enveomics collection

NCBIacc2tax.rb

Maps a list of NCBI accessions to their corresponding taxonomy using the NCBI EUtilities.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.
• Ruby gem nokogiri.
• Ruby gem json.

§ Usage

§ Arguments

Accessions

 --acc string  Comma-separated list of accessions.

Required unless 'Input file' is passed.

Input file

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

Required unless 'Accessions' is passed.

Protein

 --protein   Use if the accessions are proteins. Otherwise, accessions are assumed to be from the Nuccore Database.

Ranks

 --ranks string  Taxonomic ranks to report, separated by commas.

No header

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

Tax IDs

 --taxids   Return Taxonomy IDs instead of scientific names.

Ignore missing

 --ignore-missing   Does not report missing accessions in the output file. By default, it reports GI and empty values for all other columns.

Quiet

 --quiet   Run quietly.

Output file*

 out_file  Tab-delimited table with accessions and taxonomic classification.