ed_fasta: Export FASTA files for viral interpretation

In ecohealthalliance/eidith: Data access and analytical tools for the PREDICT EIDITH database

Export FASTA files for viral interpretation

Description

ed_fasta() and ed_fasta_group() convert a data frame to a FASTA file. ed_tests_report() is a standard report returning a data frame of all uninterpreted test sequences, along with a set of metadata, which is commonly printed to FASTA. ed_report_excel() is a convenience function for creating excel-ready CSVs for reporting. See the FASTA vignette for more guidance.

Usage

ed_fasta(
  .data,
  filename = "",
  sequence = "sequence",
  include_names = TRUE,
  ...
)

Arguments

.data	The data frame
filename	name of file to write to. If "" (default), the output is written to console.
sequence	the column name in the data frame that contains the sequence. Default is "sequence".
include_names	Whether to include column names of sequence discriptors. Default is TRUE.
...	Additional columns to include as metadata, using dplyr::select() syntax. If nothing is included, all columns are used.

Value

For ed_fasta(), ed_fasta_group(), and ed_report_excel(), the file(s) will be written to a file or the console (default). Also, a character vector of each FASTA record is returned invisibly ed_tests_report() returns a data frame.

Examples

## Not run: 
 ed_fasta(ed_tests_report())
 
## End(Not run)

ecohealthalliance/eidith documentation built on Aug. 30, 2022, 7:45 a.m.