R/SimpleGUI.R
In katrikorpela/mare: Microbiota Analysis in R Easily
Defines functions
SimpleGUI
Documented in
SimpleGUI
SimpleGUI <- function(forward.primer = NULL, name.separator = "_",
folder.name = "", usearch.path) {
all.reads <- list.files(pattern=".fastq")
rev.reads <- list.files(pattern="R2")
forward.reads <- setdiff(all.reads,rev.reads)
refDB <- system.file("extdata/silva_full.fasta",package="mare")
system(paste("mkdir ", folder.name, "ProcessedReads", sep = ""))
wd <- paste(getwd(), "/", folder.name, "ProcessedReads/", sep = "")
readnumbers <- data.frame(sample = sapply(as.character(forward.reads),
function(x) strsplit(x, split = name.separator)[[1]][1]), raw_reads = sapply(forward.reads,
function(x) length(Biostrings::readDNAStringSet(x, format = "fastq"))))
if (length(forward.primer) != 0) {
for (i in forward.reads) {
ShortRead::writeFastq(object = Biostrings::trimLRPatterns(Lpattern = forward.primer,
subject = ShortRead::readFastq(i), max.Lmismatch = 3, with.Lindels = T, Lfixed = F),
file = paste(wd, sapply(i, function(x) strsplit(x, name.separator,
fixed = F)[[1]][1]), name.separator ,"fwd.fastq", sep = ""), mode = "w",
full = F, compress = F, qualityType = "Auto")
}
} else {
for (i in seq_along(forward.reads)) {
system(paste("cp ", forward.reads[i], " ", wd, forward.reads[i], sep = ""))
}
if (length(list.files(path = wd, pattern = "*.gz$")) > 0) {
system(paste("gunzip", " ", wd, "*fastq.gz", sep = ""))
}
for (i in grep(list.files(path=wd), pattern='R2', inv=T, value=T)) {
system(paste("mv ", wd, i, " " , wd, sapply(i, function(x) strsplit(x, name.separator, fixed = F)[[1]][1]),
name.separator ,"fwd.fastq", sep = ""))
}
}
trimmed_fwd <- paste(wd, list.files(path = wd, pattern = "fwd.fastq"), sep = "")
for (i in seq_along(trimmed_fwd)) {
system(paste(usearch.path, " -fastx_truncate ", trimmed_fwd[i],
" -trunclen 150", " -fastqout ", strsplit(trimmed_fwd[i],
name.separator, fixed = T)[[1]][1], name.separator ,"truncated.fastq", sep = ""))
}
reads <- paste(wd, list.files(path = wd, pattern = "truncated.fastq"), sep = "")
for (i in seq_along(reads)) {
ShortRead::writeFasta(ShortRead::readFastq(reads[i]), file = paste(strsplit(reads[i],
split = "[.]")[[1]][1], "fasta", sep = "."))
}
reads <- paste(wd, list.files(path = wd, pattern = "*.fasta"), sep = "")
system(paste("rm ", wd, "*.fastq", sep = ""))
for (i in seq_along(reads)) {
system(paste(usearch.path, " -fastx_truncate ", reads[i], " -trunclen ",
"150", " -fastaout ", paste(strsplit(reads[i], split = ".fasta"),
"equallength.fasta", sep = name.separator), sep = ""))
}
truncatedreads <- paste(wd, list.files(path = wd, pattern = "equallength.fasta$"), sep = "")
if (length(list.files(path = wd, "fwd.fasta")) != 0) {
system(paste("rm ", wd, "*fwd.fasta", sep = ""))
}
if (length(list.files(path = wd, "truncated.fasta")) != 0) {
system(paste("rm ", wd, "*truncated.fasta", sep = ""))
}
for (i in seq_along(truncatedreads)) {
system(paste("sed '-es/^>\\(.*\\)/>\\1;barcodelabel=", strsplit(truncatedreads[i],
split = "\\_\\ProcessedReads/|\\_|\\ProcessedReads/")[[1]][2],
";/' <", truncatedreads[i], " > ", paste(strsplit(truncatedreads[i],
split = ".fasta"), "labelled.fasta", sep = name.separator), sep = ""))
}
system(paste("rm ", wd, "*equallength.fasta", sep = ""))
labelledreads <- paste(wd, list.files(path = wd, pattern = "*labelled.fasta$"), sep = "")
fl.uparse.string <- ""
for (i in seq_along(labelledreads)) {
fl.uparse.string <- paste(fl.uparse.string, labelledreads[i], sep = " ")
}
system(paste("cat ", fl.uparse.string, " > ", wd, "all.fasta", sep = ""))
dnaSet = Biostrings::readDNAStringSet(paste(wd, "all.fasta", sep = ""),
format = "fasta")
if (!is(dnaSet, "DNAStringSet")) {
dnaSet <- Biostrings::DNAStringSet(dnaSet)
}
if (is.null(names(dnaSet))) {
message("No names attribute found in dnaSet object...", "using artifically generated names")
names(dnaSet) <- paste("read", 1:length(dnaSet), sep = "-")
}
dnaSet <- suppressWarnings(dnaSet[order(dnaSet)])
counts <- BiocGenerics::table(dnaSet)
dnaSet <- unique(dnaSet)
names(dnaSet) <- paste0(paste("read", 1:length(names(dnaSet)), sep = "_"),
";size=", as.integer(counts))
dnaSet <- dnaSet[rev(order(counts))]
dnaSet <- dnaSet[as.vector(counts[rev(order(counts))] > (0.00001 * sum(counts)))]
Biostrings::writeXStringSet(dnaSet, paste(wd, "dereplicated.fasta", sep = ""),
format = "fasta")
system(paste(usearch.path, " -uchime_denovo ", wd, "dereplicated.fasta", " -nonchimeras ", wd,
"nonchimeric.fasta", sep = ""))
system(paste(usearch.path, " -cluster_otus ", wd, "nonchimeric.fasta",
" -otus ", wd, "otu.fasta", " -otu_radius_pct 3",
" -relabel OTU_", " -sizein ", " -sizeout ", sep = ""))
derep <- Biostrings::readDNAStringSet(paste(wd, "otu.fasta", sep = ""))
result <- data.frame(OTUId = names(derep))
dict <- Biostrings::PDict(derep, max.mismatch = NA, tb.end = 2)
for (i in seq_along(labelledreads)) {
seq <- Biostrings::readDNAStringSet(labelledreads[i])
result[, strsplit(labelledreads[i], split = paste("ProcessedReads/|",name.separator,sep=""))[[1]][2]] <- rowSums(Biostrings::vcountPDict(dict,
seq))
}
if (length(list.files(pattern = paste(folder.name, "TaxonomicTables", sep = ""))) == 0) {
system(paste("mkdir ", folder.name, "TaxonomicTables", sep = ""))
}
wd <- getwd()
write.table(result, paste(wd, "/", folder.name, "TaxonomicTables/", folder.name,
"_otutable.txt", sep = ""), quote = F, row.names = F, sep = "\t")
derep <- Biostrings::readDNAStringSet(paste(wd, "/", folder.name, "ProcessedReads/nonchimeric.fasta", sep = ""))
result <- data.frame(OTUId = names(derep))
dict <- Biostrings::PDict(derep, max.mismatch = NA, tb.end = 2)
for (i in seq_along(labelledreads)) {
seq <- Biostrings::readDNAStringSet(labelledreads[i])
result[, strsplit(labelledreads[i], split = paste("ProcessedReads/|",name.separator,sep=""))[[1]][2]] <- rowSums(Biostrings::vcountPDict(dict,
seq))
}
write.table(result, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
rownames(readnumbers) <- readnumbers$sample
for(i in readnumbers$sample) readnumbers[readnumbers$sample==i,"processed_reads"] <- sum(result[,i])#new
write.table(readnumbers, paste(folder.name, "readnumbers.txt",sep="_"), quote = F, row.names = F, sep = "\t")
readnumbers$raw_reads <- readnumbers$raw_reads - readnumbers$processed_reads
quartz();par(xpd = T, mar = c(9, 7, 4, 4), mgp = c(5, 1, 0))
barplot(as.matrix(t(readnumbers[, c(3, 2)])), ylab = "Number of reads",
legend.text = c("Kept", "Discarded"), args.legend = list(ncol = 2,
y = max(readnumbers$raw_reads + readnumbers$processed_reads) *
1.1, bty = "n"), col = c("royalblue", "aliceblue"), las = 2)
cat(paste("merge = F", ",",
"truncate T= ", ",",
"filter = F", ",",
"readlength = 150", ",",
"min.read.prevalence = 0.0001"),
file = paste(folder.name,"log.txt",sep="_"))
wd <- getwd()
tobeannotated <- paste(wd, "/", folder.name, "ProcessedReads/nonchimeric.fasta", sep = "")
readfile <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), check.names = F)
OTU <- ""
system(paste(usearch.path, " -utax ", tobeannotated, " -db ", refDB, " -utax_cutoff ",
"0", " -strand both -utaxout ", wd, "/", folder.name,
"TaxonomicTables/", folder.name, OTU, "taxonomy.txt", sep = ""))
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(3:4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$species <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$species[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "s:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- gsub("_","",taxonomy$species)
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "g:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "f:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "o:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "c:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "p:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- paste(taxonomy$genus, taxonomy$species, sep = ".")
taxonomy$species <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, taxonomy$species, sep = "_")
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
species_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$species),
sum)
genus_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$genus),
sum)
family_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$family),
sum)
order_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$order),
sum)
class_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$class),
sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$phylum),
sum)
write.table(species_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_species_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
}
katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.
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Defines functions SimpleGUI
Documented in SimpleGUI
SimpleGUI <- function(forward.primer = NULL, name.separator = "_",
folder.name = "", usearch.path) {
all.reads <- list.files(pattern=".fastq")
rev.reads <- list.files(pattern="R2")
forward.reads <- setdiff(all.reads,rev.reads)
refDB <- system.file("extdata/silva_full.fasta",package="mare")
system(paste("mkdir ", folder.name, "ProcessedReads", sep = ""))
wd <- paste(getwd(), "/", folder.name, "ProcessedReads/", sep = "")
readnumbers <- data.frame(sample = sapply(as.character(forward.reads),
function(x) strsplit(x, split = name.separator)[[1]][1]), raw_reads = sapply(forward.reads,
function(x) length(Biostrings::readDNAStringSet(x, format = "fastq"))))
if (length(forward.primer) != 0) {
for (i in forward.reads) {
ShortRead::writeFastq(object = Biostrings::trimLRPatterns(Lpattern = forward.primer,
subject = ShortRead::readFastq(i), max.Lmismatch = 3, with.Lindels = T, Lfixed = F),
file = paste(wd, sapply(i, function(x) strsplit(x, name.separator,
fixed = F)[[1]][1]), name.separator ,"fwd.fastq", sep = ""), mode = "w",
full = F, compress = F, qualityType = "Auto")
}
} else {
for (i in seq_along(forward.reads)) {
system(paste("cp ", forward.reads[i], " ", wd, forward.reads[i], sep = ""))
}
if (length(list.files(path = wd, pattern = "*.gz$")) > 0) {
system(paste("gunzip", " ", wd, "*fastq.gz", sep = ""))
}
for (i in grep(list.files(path=wd), pattern='R2', inv=T, value=T)) {
system(paste("mv ", wd, i, " " , wd, sapply(i, function(x) strsplit(x, name.separator, fixed = F)[[1]][1]),
name.separator ,"fwd.fastq", sep = ""))
}
}
trimmed_fwd <- paste(wd, list.files(path = wd, pattern = "fwd.fastq"), sep = "")
for (i in seq_along(trimmed_fwd)) {
system(paste(usearch.path, " -fastx_truncate ", trimmed_fwd[i],
" -trunclen 150", " -fastqout ", strsplit(trimmed_fwd[i],
name.separator, fixed = T)[[1]][1], name.separator ,"truncated.fastq", sep = ""))
}
reads <- paste(wd, list.files(path = wd, pattern = "truncated.fastq"), sep = "")
for (i in seq_along(reads)) {
ShortRead::writeFasta(ShortRead::readFastq(reads[i]), file = paste(strsplit(reads[i],
split = "[.]")[[1]][1], "fasta", sep = "."))
}
reads <- paste(wd, list.files(path = wd, pattern = "*.fasta"), sep = "")
system(paste("rm ", wd, "*.fastq", sep = ""))
for (i in seq_along(reads)) {
system(paste(usearch.path, " -fastx_truncate ", reads[i], " -trunclen ",
"150", " -fastaout ", paste(strsplit(reads[i], split = ".fasta"),
"equallength.fasta", sep = name.separator), sep = ""))
}
truncatedreads <- paste(wd, list.files(path = wd, pattern = "equallength.fasta$"), sep = "")
if (length(list.files(path = wd, "fwd.fasta")) != 0) {
system(paste("rm ", wd, "*fwd.fasta", sep = ""))
}
if (length(list.files(path = wd, "truncated.fasta")) != 0) {
system(paste("rm ", wd, "*truncated.fasta", sep = ""))
}
for (i in seq_along(truncatedreads)) {
system(paste("sed '-es/^>\\(.*\\)/>\\1;barcodelabel=", strsplit(truncatedreads[i],
split = "\\_\\ProcessedReads/|\\_|\\ProcessedReads/")[[1]][2],
";/' <", truncatedreads[i], " > ", paste(strsplit(truncatedreads[i],
split = ".fasta"), "labelled.fasta", sep = name.separator), sep = ""))
}
system(paste("rm ", wd, "*equallength.fasta", sep = ""))
labelledreads <- paste(wd, list.files(path = wd, pattern = "*labelled.fasta$"), sep = "")
fl.uparse.string <- ""
for (i in seq_along(labelledreads)) {
fl.uparse.string <- paste(fl.uparse.string, labelledreads[i], sep = " ")
}
system(paste("cat ", fl.uparse.string, " > ", wd, "all.fasta", sep = ""))
dnaSet = Biostrings::readDNAStringSet(paste(wd, "all.fasta", sep = ""),
format = "fasta")
if (!is(dnaSet, "DNAStringSet")) {
dnaSet <- Biostrings::DNAStringSet(dnaSet)
}
if (is.null(names(dnaSet))) {
message("No names attribute found in dnaSet object...", "using artifically generated names")
names(dnaSet) <- paste("read", 1:length(dnaSet), sep = "-")
}
dnaSet <- suppressWarnings(dnaSet[order(dnaSet)])
counts <- BiocGenerics::table(dnaSet)
dnaSet <- unique(dnaSet)
names(dnaSet) <- paste0(paste("read", 1:length(names(dnaSet)), sep = "_"),
";size=", as.integer(counts))
dnaSet <- dnaSet[rev(order(counts))]
dnaSet <- dnaSet[as.vector(counts[rev(order(counts))] > (0.00001 * sum(counts)))]
Biostrings::writeXStringSet(dnaSet, paste(wd, "dereplicated.fasta", sep = ""),
format = "fasta")
system(paste(usearch.path, " -uchime_denovo ", wd, "dereplicated.fasta", " -nonchimeras ", wd,
"nonchimeric.fasta", sep = ""))
system(paste(usearch.path, " -cluster_otus ", wd, "nonchimeric.fasta",
" -otus ", wd, "otu.fasta", " -otu_radius_pct 3",
" -relabel OTU_", " -sizein ", " -sizeout ", sep = ""))
derep <- Biostrings::readDNAStringSet(paste(wd, "otu.fasta", sep = ""))
result <- data.frame(OTUId = names(derep))
dict <- Biostrings::PDict(derep, max.mismatch = NA, tb.end = 2)
for (i in seq_along(labelledreads)) {
seq <- Biostrings::readDNAStringSet(labelledreads[i])
result[, strsplit(labelledreads[i], split = paste("ProcessedReads/|",name.separator,sep=""))[[1]][2]] <- rowSums(Biostrings::vcountPDict(dict,
seq))
}
if (length(list.files(pattern = paste(folder.name, "TaxonomicTables", sep = ""))) == 0) {
system(paste("mkdir ", folder.name, "TaxonomicTables", sep = ""))
}
wd <- getwd()
write.table(result, paste(wd, "/", folder.name, "TaxonomicTables/", folder.name,
"_otutable.txt", sep = ""), quote = F, row.names = F, sep = "\t")
derep <- Biostrings::readDNAStringSet(paste(wd, "/", folder.name, "ProcessedReads/nonchimeric.fasta", sep = ""))
result <- data.frame(OTUId = names(derep))
dict <- Biostrings::PDict(derep, max.mismatch = NA, tb.end = 2)
for (i in seq_along(labelledreads)) {
seq <- Biostrings::readDNAStringSet(labelledreads[i])
result[, strsplit(labelledreads[i], split = paste("ProcessedReads/|",name.separator,sep=""))[[1]][2]] <- rowSums(Biostrings::vcountPDict(dict,
seq))
}
write.table(result, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
rownames(readnumbers) <- readnumbers$sample
for(i in readnumbers$sample) readnumbers[readnumbers$sample==i,"processed_reads"] <- sum(result[,i])#new
write.table(readnumbers, paste(folder.name, "readnumbers.txt",sep="_"), quote = F, row.names = F, sep = "\t")
readnumbers$raw_reads <- readnumbers$raw_reads - readnumbers$processed_reads
quartz();par(xpd = T, mar = c(9, 7, 4, 4), mgp = c(5, 1, 0))
barplot(as.matrix(t(readnumbers[, c(3, 2)])), ylab = "Number of reads",
legend.text = c("Kept", "Discarded"), args.legend = list(ncol = 2,
y = max(readnumbers$raw_reads + readnumbers$processed_reads) *
1.1, bty = "n"), col = c("royalblue", "aliceblue"), las = 2)
cat(paste("merge = F", ",",
"truncate T= ", ",",
"filter = F", ",",
"readlength = 150", ",",
"min.read.prevalence = 0.0001"),
file = paste(folder.name,"log.txt",sep="_"))
wd <- getwd()
tobeannotated <- paste(wd, "/", folder.name, "ProcessedReads/nonchimeric.fasta", sep = "")
readfile <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), check.names = F)
OTU <- ""
system(paste(usearch.path, " -utax ", tobeannotated, " -db ", refDB, " -utax_cutoff ",
"0", " -strand both -utaxout ", wd, "/", folder.name,
"TaxonomicTables/", folder.name, OTU, "taxonomy.txt", sep = ""))
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(3:4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$species <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$species[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "s:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- gsub("_","",taxonomy$species)
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "g:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "f:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "o:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "c:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "p:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- paste(taxonomy$genus, taxonomy$species, sep = ".")
taxonomy$species <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, taxonomy$species, sep = "_")
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
species_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$species),
sum)
genus_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$genus),
sum)
family_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$family),
sum)
order_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$order),
sum)
class_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$class),
sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$phylum),
sum)
write.table(species_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_species_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
}
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