cluster sequences from fasta file, and return file

cluster sequences from fasta file, and return tibble

cluster sequences from fasta tibble, and return file

vs_cluster_unoise returns NULL and warning when no clusters found

test_that("error when wrong output_format", {
"Invalid output_format. Choose from 'fasta' or 'fastq'.")
test_that("error when output_format is 'fasta', and fastqout is defined", {
"When output_format is 'fasta', 'fastqout' cannot be used. Use 'fastaout' instead.")
test_that("error when output_format is 'fastq', and fastaout is defined", {
"When output_format is 'fastq', 'fastaout' cannot be used. Use 'fastqout' instead.")
test_that("error when input file does not exist", {
paste("Cannot find input FASTQ file:", fastq_input))
test_that("error when reverse file does not exist", {
paste("Cannot find reverse FASTQ file:", reverse))
test_that("fastq_input and reverse can be joined when files, and results written to fastq file", {
return_value <- vs_fastq_join(fastq_input = fastq_input,
"No reverse reads provided. Please supply reverse or use a 'pe_df' object.")
test_that("fastq_input and reverse can be joined when files, and results written to fasta file", {
test_that("fastq_input and reverse can be joined when files, and results given as fastq tibble", {
joined <- vs_fastq_join(fastq_input = fastq_input,
test_that("fastq_input and reverse can be joined when files, and results given as fasta tibble", {
test_that("fastq_input and reverse can be joined when tibbles, and results written to fastq file", {
test_that("fastq_input and reverse can be joined when tibbles, and results given as tibble", {
test_that("log file exists when specified", {
test_that("fastq_input and reverse can be joined when files, and results given as fastq tibble with vsearch_options", {
test_that("join fastq sequences from a pe_df data frame", {
joined <- vs_fastq_join(fastq_input = fastq_input)
"fastq_input has class 'pe_df' but no 'reverse' attribute found.")

"Invalid output_format. Choose from 'fasta' or 'fastq'."
"error when output_format is 'fasta', and fastqout is defined"
"When output_format is 'fasta', 'fastqout' cannot be used. Use 'fastaout' instead."
"error when output_format is 'fastq', and fastaout is defined"
"When output_format is 'fastq', 'fastaout' cannot be used. Use 'fastqout' instead."
"error when reverse file does not exist"
"fastq_input and reverse can be joined when files, and results written to fastq file"
"No reverse reads provided. Please supply reverse or use a 'pe_df' object."
"fastq_input and reverse can be joined when files, and results written to fasta file"
"fastq_input and reverse can be joined when files, and results given as fastq tibble"
"fastq_input and reverse can be joined when files, and results given as fasta tibble"
"fastq_input and reverse can be joined when tibbles, and results written to fastq file"
"fastq_input and reverse can be joined when tibbles, and results given as tibble"
"fastq_input and reverse can be joined when files, and results given as fastq tibble with vsearch_options"
"join fastq sequences from a pe_df data frame"
"fastq_input has class 'pe_df' but no 'reverse' attribute found."