ktGetTaxInfo1
Explore hierarchical metagenomic data with zoomable pie charts
Overview
Description:
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Retrieves taxonomy information for accessions or taxonomy IDs (as arguments or the first field of <stdin>, separated by whitespace). If the input is a number, it is assumed to be a taxonomy ID; otherwise it will be considered an accession or sequence ID containing an accession in the fourth field of pipe notation (e.g. "gi|12345|xx|ABC123.1|", ignoring fasta/fastq tag markers [>,@]). If taxonomy information was not found for a given input line, the output line will be only the taxonomy ID, which will be 0 if it was looked up from an accession but not found.
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Output fields are: taxID depth parent rank name
Usage:
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ktGetTaxInfo [IDs ...] [< ID_list] > tax_info |
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Command line example: |
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ktGetTaxInfo A00001.1 "gi|2|emb|A00002.1|" 9606 |
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Fasta tag example: |
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grep ">" sequence.fasta | ktGetTaxInfo |
Options
[-p]
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Prepend tax info to the original lines (separated by tabs). |
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[-a]
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Append tax info 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.