parse_greengenes: Parse Greengenes release

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Parse Greengenes release

Description

Parses the greengenes database.

Usage

parse_greengenes(tax_file, seq_file = NULL)

Arguments

tax_file	(character of length 1) The file path to the greengenes taxonomy file.
seq_file	(character of length 1) The file path to the greengenes sequence fasta file. This is optional.

Details

The taxonomy input file has a format like:

228054  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synech...
844608  k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synech...
...

The optional sequence file has a format like:

>1111886
AACGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGAGACCTTCGGGTCTAGTGGCGCACGGGTGCGTA...
>1111885
AGAGTTTGATCCTGGCTCAGAATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTACGAGAAATCCCGAGC...
...

Value

taxmap

See Also

Other parsers: extract_tax_data(), lookup_tax_data(), parse_dada2(), parse_edge_list(), parse_mothur_tax_summary(), parse_mothur_taxonomy(), parse_newick(), parse_phylo(), parse_phyloseq(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome(), parse_unite_general()

metacoder documentation built on April 3, 2025, 8:39 p.m.