ktGetTaxInfo - explore hierarchical metagenomic data with zoomable
pie charts
Description:
- 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.
- Output fields are: taxID depth parent rank name
Usage:
- ktGetTaxInfo [IDs ...] [< ID_list] > tax_info
- Command line example:
- ktGetTaxInfo A00001.1 "gi|2|emb|A00002.1|" 9606
- Fasta tag example:
- grep ">" sequence.fasta | ktGetTaxInfo
- [-p]
- Prepend tax info to the original lines (separated by tabs).
- [-a]
- Append tax info 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.