ktGetTaxIDFromAcc1

Overview

Description:

Translates accessions (from arguments or <stdin>) to NCBI taxonomy IDs. The accession can be bare or in the fourth field of pipe notation (e.g. "gi|12345|xx|ABC123.1|", ignoring fasta tag markers [">"]). Inputs that are bare numbers will be assumed to be taxonomy IDs already and preserved. Accessions with no taxonomy IDs in the database will return 0.

Usage:

ktGetTaxIDFromAcc [options] [acc1 acc2 ...] [< acc_list] > tax_ID_list

Command line example:

ktGetTaxIDFromAcc A00001.1 A00002.1

Fasta tag example:

grep ">" sequence | ktGetTaxIDFromAcc > sequence.tax

Options

[-p]

Prepend tax IDs to the original lines (separated by tabs).

[-a]

Append tax IDs to the original lines (separated by tabs).

[-f] <integer>

Field of accessions. [Default: '1']

[-tax <string>

Path to directory containing a taxonomy database to use.