parse_greengenes

0th

Percentile

Parse Greengenes release

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: parse_dada2(), parse_edge_list(), parse_mothur_tax_summary(), parse_mothur_taxonomy(), parse_newick(), parse_phyloseq(), parse_phylo(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_ubiome(), parse_unite_general()

Aliases
  • parse_greengenes
Documentation reproduced from package metacoder, version 0.3.4, License: GPL-2 | GPL-3

Community examples

Looks like there are no examples yet.