ktGetTaxIDFromAcc1
Explore hierarchical metagenomic data with zoomable pie charts
Overview
Description:
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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:
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ktGetTaxIDFromAcc [options] [acc1 acc2 ...] [< acc_list] > tax_ID_list |
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Command line example: |
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ktGetTaxIDFromAcc A00001.1 A00002.1 |
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Fasta tag example: |
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grep ">" sequence | ktGetTaxIDFromAcc > sequence.tax |
Options
[-p]
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Prepend tax IDs to the original lines (separated by tabs). |
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[-a]
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Append tax IDs to the original lines (separated by tabs). |
[-f] <integer>
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Field of accessions. [Default: '1'] |
[-tax <string>
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Path to directory containing a taxonomy database to use. |
Releases
3 releases since Debian 11 (Bullseye); the text changed 1 time.
-a until Debian 11 (Bullseye);
-p until Debian 11 (Bullseye).