append

Behavior:

• Retrieves taxonomic information from the local taxonomy database.
• Appends scientific names and/or taxon IDs of specified ranks to each row.
• If --rank is not specified, appends the scientific name of the input taxon.
• Header lines (starting with “#”) are processed to append appropriate column names.

Valid ranks:

• species, genus, family, order, class, phylum, kingdom
• Other ranks (e.g., clade, no rank) may work but are not officially supported.

Input:

• Accepts one or more TSV files as input.
• Reads from standard input if “stdin” is specified.
• The input file should contain taxon IDs or scientific names in a specific column.

Output:

• Tab-separated values with appended rank columns.
• By default, output is written to standard output.
• Use --outfile to write to a file instead.

Examples:

1. Append scientific names for specified ranks nwr append input.tsv --rank genus --rank family

2. Append both names and IDs nwr append input.tsv --rank species --id

3. Read from stdin, append genus information cat input.tsv | nwr append stdin --rank genus

4. Specify column and output file nwr append input.tsv -c 2 --rank kingdom -o output.tsv