Enveomics collection

gi2tax.rb

Maps a list of NCBI GIs 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

GIs

 --gis string  Comma-separated list of GIs.

Required unless 'Input file' is passed.

Input file

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

Required unless 'GIs' is passed.

Protein

 --protein   Use if the GIs are proteins. Otherwise, GIs 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.

Exact GI

 --exact-gi   Returns only taxonomy associated with the exact GI passed. By default, it attempts to update accession versions if possible.

Ignore missing

 --ignore-missing   Does not report missing GIs 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 GIs and taxonomic classification.