R/FormatRefDB.R
In katrikorpela/mare: Microbiota Analysis in R Easily
Defines functions
FormatRefDB
Documented in
FormatRefDB
FormatRefDB <- function(refDB, usearch.path, confidence.file, gut.specific = F,
taxman = F, named.species = F) {
if (taxman) {
system(paste("cp ", refDB, " refDB.fasta", sep = ""))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/;/,/g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/ //g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/subsp./subsp/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/Bacteria/;tax=d:Bacteria/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/Bacteria,/Bacteria,p:/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[(]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[)]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[|]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[/]/_/g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[-]//g"), "refDB.fasta"))
database <- seqinr::read.fasta("refDB.fasta", as.string = T, forceDNAtolower = F)
for (i in seq_along(names(database))) {
names(database)[i] <- paste(strsplit(names(database)[i], split = ",")[[1]][1],
",", strsplit(names(database)[i], split = ",")[[1]][2], ",c:",
strsplit(names(database)[i], split = ",")[[1]][3], ",o:", strsplit(names(database)[i],
split = ",")[[1]][4], ",f:", strsplit(names(database)[i],
split = ",")[[1]][5], ",g:", strsplit(names(database)[i],
split = ",")[[1]][6], ",s:", strsplit(names(database)[i],
split = ",")[[1]][7], sep = "")
}
database <- database[names(database)[grepl(":NA", names(database), fixed = T) == F]]
database <- database[names(database)[grepl(":,", names(database), fixed = T) == F]]
if (named.species) {
database <- database[names(database)[grepl("uncultured", names(database)) == F]]
database <- database[names(database)[grepl("unidentified", names(database)) == F]]
database <- database[names(database)[grepl("s:bacterium", names(database)) == F]]
database <- database[names(database)[grepl("metagenome", names(database)) == F]]
database <- database[names(database)[grepl("sp.", names(database), fixed = T) == F]]
}
if (gut.specific) {
databasetaxonomy <- data.frame(p = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][2]), c = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][3]), o = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][4]), f = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][5]), g = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][6]), s = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][7]))
databaseselected <- database[databasetaxonomy$g == "g:Millisia" |
databasetaxonomy$g == "g:Succinivibrio" |
databasetaxonomy$g == "g:Parabacteroides" |
databasetaxonomy$g == "g:Paraprevotella" |
databasetaxonomy$g == "g:Treponema" |
databasetaxonomy$g == "g:Fibrobacter" |
databasetaxonomy$g == "g:Methanobrevibacter" |
databasetaxonomy$g == "g:Butyricoccus" |
databasetaxonomy$g == "g:Phascolarctobacterium" |
databasetaxonomy$g == "g:Butyricimonas" |
databasetaxonomy$g == "g:Turicibacter" |
databasetaxonomy$g == "g:Odoribacter" |
databasetaxonomy$g == "g:Rhodococcus" | databasetaxonomy$g ==
"g:Actinomyces" | databasetaxonomy$g == "g:Bifidobacterium" |
databasetaxonomy$g == "g:Corynebacterium" | databasetaxonomy$g ==
"g:Micrococcus" | databasetaxonomy$g == "g:Rothia" | databasetaxonomy$g ==
"g:Mycobacterium" | databasetaxonomy$g == "g:Propionibacterium" |
databasetaxonomy$g == "g:Streptomyces" | databasetaxonomy$f ==
"f:Coriobacteriaceae" | databasetaxonomy$g == "g:Alcaligenes" |
databasetaxonomy$g == "g:Gemmiger" |
databasetaxonomy$g == "g:Bordetella" | databasetaxonomy$g ==
"g:Parasutterella" | databasetaxonomy$g == "g:Sutterella" |
databasetaxonomy$g == "g:Burkholderia" | databasetaxonomy$g ==
"g:Ralstonia" | databasetaxonomy$g == "g:Neisseria" | databasetaxonomy$g ==
"g:Oxalobacter" | databasetaxonomy$g == "g:Aeromonas" | databasetaxonomy$g ==
"g:Granulicatella" | databasetaxonomy$g == "g:Citrobacter" |
databasetaxonomy$g == "g:Enterobacter" | databasetaxonomy$g ==
"g:Escherichia-Shigella" | databasetaxonomy$g == "g:Klebsiella" |
databasetaxonomy$g == "g:Leminorella" | databasetaxonomy$g ==
"g:Morganella" | databasetaxonomy$g == "g:Proteus" | databasetaxonomy$g ==
"g:Salmonella" | databasetaxonomy$g == "g:Serratia" | databasetaxonomy$g ==
"g:Yersinia" | databasetaxonomy$g == "g:Pasteurella" | databasetaxonomy$g ==
"g:Haemophilus" | databasetaxonomy$g == "g:Pseudomonas" | databasetaxonomy$g ==
"g:Bilophila" | databasetaxonomy$g == "g:Desulfovibrio" | databasetaxonomy$g ==
"g:Campylobacter" | databasetaxonomy$g == "g:Helicobacter" |
databasetaxonomy$g == "g:Fusobacterium" | databasetaxonomy$g ==
"g:Bacteroides" | databasetaxonomy$f == "f:Porphyromonadaceae" |
databasetaxonomy$f == "f:Prevotellaceae" | databasetaxonomy$g ==
"g:Alistipes" | databasetaxonomy$g == "g:Aerococcus" | databasetaxonomy$g ==
"g:Bacillus" | databasetaxonomy$g == "g:Enterococcus" | databasetaxonomy$f ==
"f:Lactobacillaceae" | databasetaxonomy$g == "g:Listeria" |
databasetaxonomy$g == "g:Akkermansia" | databasetaxonomy$g ==
"g:Staphylococcus" | databasetaxonomy$f == "f:Streptococcaceae" |
databasetaxonomy$g == "g:Leuconostoc" | databasetaxonomy$g ==
"g:Weissella" | databasetaxonomy$f == "f:Christensenellaceae" |
databasetaxonomy$g == "g:Clostridium" | databasetaxonomy$g ==
"g:Anaerofustis" | databasetaxonomy$g == "g:Eubacterium" |
databasetaxonomy$g == "g:Anaerococcus" | databasetaxonomy$g ==
"g:Finegoldia" | databasetaxonomy$g == "g:Gemella" | databasetaxonomy$g ==
"g:IncertaeSedis" |
databasetaxonomy$g == "g:Parvimonas" | databasetaxonomy$g ==
"g:Peptoniphilus" | databasetaxonomy$g == "g:Tissierella" |
databasetaxonomy$g == "g:Anaerosporobacter" | databasetaxonomy$g ==
"g:Anaerostipes" | databasetaxonomy$g == "g:Blautia" | databasetaxonomy$g ==
"g:Butyrivibrio" | databasetaxonomy$g == "g:Coprococcus" |
databasetaxonomy$g == "g:Dorea" | databasetaxonomy$g ==
"g:Lachnospira" |
databasetaxonomy$g == "g:Roseburia" | databasetaxonomy$g ==
"g:Peptostreptococcus" | databasetaxonomy$g == "g:Sporacetigenium" |
databasetaxonomy$f == "f:Erysipelotrichaceae" |
databasetaxonomy$f == "f:Lachnospiraceae" |
databasetaxonomy$f == "f:Ruminococcaceae" |
databasetaxonomy$f == "f:Veillonellaceae" |
databasetaxonomy$f == "f:Acidaminococcaceae" | databasetaxonomy$g == "g:Veillonella" |
databasetaxonomy$g == "g:Allisonella" | databasetaxonomy$g ==
"g:Dialister" | databasetaxonomy$g == "g:Megamonas" | databasetaxonomy$g ==
"g:Megasphaera" | databasetaxonomy$g == "g:Mitsuokella" | databasetaxonomy$g ==
"g:Anaerotruncus" | databasetaxonomy$g == "g:Faecalibacterium" |
databasetaxonomy$g == "g:Flavonifractor" | databasetaxonomy$g ==
"g:Oscillibacter" | databasetaxonomy$g == "g:Oscillospira" |
databasetaxonomy$g == "g:Ruminococcus" | databasetaxonomy$g ==
"g:Pseudoflavonifractor" | databasetaxonomy$g == "g:Sporobacter" |
databasetaxonomy$g == "g:Subdoligranulum" | databasetaxonomy$g ==
"g:Butyricicoccus" | databasetaxonomy$g == "g:Anaerofilum"]
seqinr::write.fasta(sequences = databaseselected, file.out = "GutDB.fasta",
names = paste(names(databaseselected), ";", sep = ""), as.string = T)
system(paste("sed -i", shQuote(""), "-E", shQuote("s/tax=d:Bacteria;//g"),
"GutDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/:,/:NA,/g"),
"GutDB.fasta"))
system(paste(usearch.path, " -makeudb_utax ", "GutDB.fasta", " -output ",
"GutDB.udb", " -taxconfsin ", confidence.file, sep = ""))
} else {
seqinr::write.fasta(sequences = database, file.out = "refDB.fasta",
names = paste(names(database), ";", sep = ""), as.string = T)
system(paste("sed -i", shQuote(""), "-E", shQuote("s/tax=d:Bacteria;//g"),
"refDB.fasta"))
system(paste(usearch.path, " -makeudb_utax ", "refDB.fasta", " -output ",
"refDB.udb", " -taxconfsin ", confidence.file, sep = ""))
}
} else {
if (gut.specific) {
database <- seqinr::read.fasta(refDB, as.string = T, forceDNAtolower = F)
databasetaxonomy <- data.frame(p = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][2]), c = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][3]), o = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][4]), f = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][5]), g = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][6]))
databaseselected <- database[databasetaxonomy$g == "g:Gemmiger;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Succinivibrio" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parabacteroides" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Paraprevotella" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Treponema" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Fibrobacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Methanobrevibacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricoccus" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Phascolarctobacterium" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricimonas" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Turicibacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Odoribacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Millisia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Rhodococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Actinomyces;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bifidobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Corynebacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Micrococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Rothia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Mycobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Propionibacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Streptomyces;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Coriobacteriaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Alcaligenes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bordetella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parasutterella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sutterella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Burkholderia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Ralstonia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Neisseria;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oxalobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Aeromonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Granulicatella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Citrobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Enterobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Escherichia-Shigella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Klebsiella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Leminorella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Morganella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Proteus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Salmonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Serratia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Yersinia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pasteurella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Haemophilus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pseudomonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bilophila;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Desulfovibrio;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Campylobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Helicobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Fusobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bacteroides;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Porphyromonadaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$f == "f:Prevotellaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Alistipes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Aerococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bacillus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Enterococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Lactobacillaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Listeria;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Akkermansia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Staphylococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Streptococcaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Leuconostoc;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Weissella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Christensenellaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Clostridium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerofustis;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Eubacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Finegoldia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Gemella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:IncertaeSedis;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parvimonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Peptoniphilus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Tissierella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerosporobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerostipes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Blautia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyrivibrio;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Coprococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Dorea;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Lachnospira;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Roseburia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Peptostreptococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sporacetigenium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Erysipelotrichaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$f == "f:Acidaminococcaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Veillonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Allisonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Dialister;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Megamonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Megasphaera;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Mitsuokella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerotruncus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Faecalibacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Flavonifractor;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oscillibacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oscillospira;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Ruminococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pseudoflavonifractor;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sporobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Subdoligranulum;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricicoccus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerofilum;" &
!is.na(databasetaxonomy$g)]
seqinr::write.fasta(sequences = na.omit(databaseselected), file.out = "GutDB.fasta",
names = names(databaseselected), as.string = T)
system(paste(usearch.path, " -makeudb_utax ", "GutDB.fasta", " -output ",
"GutDB.udb", " -taxconfsin ", confidence.file, sep = ""))
} else {
system(paste(usearch.path, " -makeudb_utax ", refDB, " -output ",
"refDB.udb", " -taxconfsin ", confidence.file, sep = ""))
}
}
}
katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.
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Defines functions FormatRefDB
Documented in FormatRefDB
FormatRefDB <- function(refDB, usearch.path, confidence.file, gut.specific = F,
taxman = F, named.species = F) {
if (taxman) {
system(paste("cp ", refDB, " refDB.fasta", sep = ""))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/;/,/g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/ //g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/subsp./subsp/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/Bacteria/;tax=d:Bacteria/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/Bacteria,/Bacteria,p:/g"),
"refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[(]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[)]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[|]//g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[/]/_/g"), "refDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/[-]//g"), "refDB.fasta"))
database <- seqinr::read.fasta("refDB.fasta", as.string = T, forceDNAtolower = F)
for (i in seq_along(names(database))) {
names(database)[i] <- paste(strsplit(names(database)[i], split = ",")[[1]][1],
",", strsplit(names(database)[i], split = ",")[[1]][2], ",c:",
strsplit(names(database)[i], split = ",")[[1]][3], ",o:", strsplit(names(database)[i],
split = ",")[[1]][4], ",f:", strsplit(names(database)[i],
split = ",")[[1]][5], ",g:", strsplit(names(database)[i],
split = ",")[[1]][6], ",s:", strsplit(names(database)[i],
split = ",")[[1]][7], sep = "")
}
database <- database[names(database)[grepl(":NA", names(database), fixed = T) == F]]
database <- database[names(database)[grepl(":,", names(database), fixed = T) == F]]
if (named.species) {
database <- database[names(database)[grepl("uncultured", names(database)) == F]]
database <- database[names(database)[grepl("unidentified", names(database)) == F]]
database <- database[names(database)[grepl("s:bacterium", names(database)) == F]]
database <- database[names(database)[grepl("metagenome", names(database)) == F]]
database <- database[names(database)[grepl("sp.", names(database), fixed = T) == F]]
}
if (gut.specific) {
databasetaxonomy <- data.frame(p = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][2]), c = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][3]), o = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][4]), f = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][5]), g = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][6]), s = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][7]))
databaseselected <- database[databasetaxonomy$g == "g:Millisia" |
databasetaxonomy$g == "g:Succinivibrio" |
databasetaxonomy$g == "g:Parabacteroides" |
databasetaxonomy$g == "g:Paraprevotella" |
databasetaxonomy$g == "g:Treponema" |
databasetaxonomy$g == "g:Fibrobacter" |
databasetaxonomy$g == "g:Methanobrevibacter" |
databasetaxonomy$g == "g:Butyricoccus" |
databasetaxonomy$g == "g:Phascolarctobacterium" |
databasetaxonomy$g == "g:Butyricimonas" |
databasetaxonomy$g == "g:Turicibacter" |
databasetaxonomy$g == "g:Odoribacter" |
databasetaxonomy$g == "g:Rhodococcus" | databasetaxonomy$g ==
"g:Actinomyces" | databasetaxonomy$g == "g:Bifidobacterium" |
databasetaxonomy$g == "g:Corynebacterium" | databasetaxonomy$g ==
"g:Micrococcus" | databasetaxonomy$g == "g:Rothia" | databasetaxonomy$g ==
"g:Mycobacterium" | databasetaxonomy$g == "g:Propionibacterium" |
databasetaxonomy$g == "g:Streptomyces" | databasetaxonomy$f ==
"f:Coriobacteriaceae" | databasetaxonomy$g == "g:Alcaligenes" |
databasetaxonomy$g == "g:Gemmiger" |
databasetaxonomy$g == "g:Bordetella" | databasetaxonomy$g ==
"g:Parasutterella" | databasetaxonomy$g == "g:Sutterella" |
databasetaxonomy$g == "g:Burkholderia" | databasetaxonomy$g ==
"g:Ralstonia" | databasetaxonomy$g == "g:Neisseria" | databasetaxonomy$g ==
"g:Oxalobacter" | databasetaxonomy$g == "g:Aeromonas" | databasetaxonomy$g ==
"g:Granulicatella" | databasetaxonomy$g == "g:Citrobacter" |
databasetaxonomy$g == "g:Enterobacter" | databasetaxonomy$g ==
"g:Escherichia-Shigella" | databasetaxonomy$g == "g:Klebsiella" |
databasetaxonomy$g == "g:Leminorella" | databasetaxonomy$g ==
"g:Morganella" | databasetaxonomy$g == "g:Proteus" | databasetaxonomy$g ==
"g:Salmonella" | databasetaxonomy$g == "g:Serratia" | databasetaxonomy$g ==
"g:Yersinia" | databasetaxonomy$g == "g:Pasteurella" | databasetaxonomy$g ==
"g:Haemophilus" | databasetaxonomy$g == "g:Pseudomonas" | databasetaxonomy$g ==
"g:Bilophila" | databasetaxonomy$g == "g:Desulfovibrio" | databasetaxonomy$g ==
"g:Campylobacter" | databasetaxonomy$g == "g:Helicobacter" |
databasetaxonomy$g == "g:Fusobacterium" | databasetaxonomy$g ==
"g:Bacteroides" | databasetaxonomy$f == "f:Porphyromonadaceae" |
databasetaxonomy$f == "f:Prevotellaceae" | databasetaxonomy$g ==
"g:Alistipes" | databasetaxonomy$g == "g:Aerococcus" | databasetaxonomy$g ==
"g:Bacillus" | databasetaxonomy$g == "g:Enterococcus" | databasetaxonomy$f ==
"f:Lactobacillaceae" | databasetaxonomy$g == "g:Listeria" |
databasetaxonomy$g == "g:Akkermansia" | databasetaxonomy$g ==
"g:Staphylococcus" | databasetaxonomy$f == "f:Streptococcaceae" |
databasetaxonomy$g == "g:Leuconostoc" | databasetaxonomy$g ==
"g:Weissella" | databasetaxonomy$f == "f:Christensenellaceae" |
databasetaxonomy$g == "g:Clostridium" | databasetaxonomy$g ==
"g:Anaerofustis" | databasetaxonomy$g == "g:Eubacterium" |
databasetaxonomy$g == "g:Anaerococcus" | databasetaxonomy$g ==
"g:Finegoldia" | databasetaxonomy$g == "g:Gemella" | databasetaxonomy$g ==
"g:IncertaeSedis" |
databasetaxonomy$g == "g:Parvimonas" | databasetaxonomy$g ==
"g:Peptoniphilus" | databasetaxonomy$g == "g:Tissierella" |
databasetaxonomy$g == "g:Anaerosporobacter" | databasetaxonomy$g ==
"g:Anaerostipes" | databasetaxonomy$g == "g:Blautia" | databasetaxonomy$g ==
"g:Butyrivibrio" | databasetaxonomy$g == "g:Coprococcus" |
databasetaxonomy$g == "g:Dorea" | databasetaxonomy$g ==
"g:Lachnospira" |
databasetaxonomy$g == "g:Roseburia" | databasetaxonomy$g ==
"g:Peptostreptococcus" | databasetaxonomy$g == "g:Sporacetigenium" |
databasetaxonomy$f == "f:Erysipelotrichaceae" |
databasetaxonomy$f == "f:Lachnospiraceae" |
databasetaxonomy$f == "f:Ruminococcaceae" |
databasetaxonomy$f == "f:Veillonellaceae" |
databasetaxonomy$f == "f:Acidaminococcaceae" | databasetaxonomy$g == "g:Veillonella" |
databasetaxonomy$g == "g:Allisonella" | databasetaxonomy$g ==
"g:Dialister" | databasetaxonomy$g == "g:Megamonas" | databasetaxonomy$g ==
"g:Megasphaera" | databasetaxonomy$g == "g:Mitsuokella" | databasetaxonomy$g ==
"g:Anaerotruncus" | databasetaxonomy$g == "g:Faecalibacterium" |
databasetaxonomy$g == "g:Flavonifractor" | databasetaxonomy$g ==
"g:Oscillibacter" | databasetaxonomy$g == "g:Oscillospira" |
databasetaxonomy$g == "g:Ruminococcus" | databasetaxonomy$g ==
"g:Pseudoflavonifractor" | databasetaxonomy$g == "g:Sporobacter" |
databasetaxonomy$g == "g:Subdoligranulum" | databasetaxonomy$g ==
"g:Butyricicoccus" | databasetaxonomy$g == "g:Anaerofilum"]
seqinr::write.fasta(sequences = databaseselected, file.out = "GutDB.fasta",
names = paste(names(databaseselected), ";", sep = ""), as.string = T)
system(paste("sed -i", shQuote(""), "-E", shQuote("s/tax=d:Bacteria;//g"),
"GutDB.fasta"))
system(paste("sed -i", shQuote(""), "-E", shQuote("s/:,/:NA,/g"),
"GutDB.fasta"))
system(paste(usearch.path, " -makeudb_utax ", "GutDB.fasta", " -output ",
"GutDB.udb", " -taxconfsin ", confidence.file, sep = ""))
} else {
seqinr::write.fasta(sequences = database, file.out = "refDB.fasta",
names = paste(names(database), ";", sep = ""), as.string = T)
system(paste("sed -i", shQuote(""), "-E", shQuote("s/tax=d:Bacteria;//g"),
"refDB.fasta"))
system(paste(usearch.path, " -makeudb_utax ", "refDB.fasta", " -output ",
"refDB.udb", " -taxconfsin ", confidence.file, sep = ""))
}
} else {
if (gut.specific) {
database <- seqinr::read.fasta(refDB, as.string = T, forceDNAtolower = F)
databasetaxonomy <- data.frame(p = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][2]), c = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][3]), o = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][4]), f = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][5]), g = sapply(names(database), function(x) strsplit(x,
split = ",")[[1]][6]))
databaseselected <- database[databasetaxonomy$g == "g:Gemmiger;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Succinivibrio" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parabacteroides" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Paraprevotella" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Treponema" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Fibrobacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Methanobrevibacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricoccus" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Phascolarctobacterium" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricimonas" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Turicibacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Odoribacter" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Millisia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Rhodococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Actinomyces;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bifidobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Corynebacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Micrococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Rothia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Mycobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Propionibacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Streptomyces;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Coriobacteriaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Alcaligenes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bordetella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parasutterella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sutterella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Burkholderia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Ralstonia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Neisseria;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oxalobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Aeromonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Granulicatella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Citrobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Enterobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Escherichia-Shigella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Klebsiella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Leminorella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Morganella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Proteus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Salmonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Serratia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Yersinia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pasteurella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Haemophilus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pseudomonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bilophila;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Desulfovibrio;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Campylobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Helicobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Fusobacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bacteroides;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Porphyromonadaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$f == "f:Prevotellaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Alistipes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Aerococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Bacillus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Enterococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Lactobacillaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Listeria;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Akkermansia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Staphylococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Streptococcaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Leuconostoc;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Weissella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Christensenellaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Clostridium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerofustis;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Eubacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Finegoldia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Gemella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:IncertaeSedis;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Parvimonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Peptoniphilus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Tissierella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerosporobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerostipes;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Blautia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyrivibrio;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Coprococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Dorea;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Lachnospira;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Roseburia;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Peptostreptococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sporacetigenium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$f == "f:Erysipelotrichaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$f == "f:Acidaminococcaceae" &
!is.na(databasetaxonomy$f) | databasetaxonomy$g == "g:Veillonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Allisonella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Dialister;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Megamonas;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Megasphaera;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Mitsuokella;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerotruncus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Faecalibacterium;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Flavonifractor;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oscillibacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Oscillospira;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Ruminococcus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Pseudoflavonifractor;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Sporobacter;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Subdoligranulum;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Butyricicoccus;" &
!is.na(databasetaxonomy$g) | databasetaxonomy$g == "g:Anaerofilum;" &
!is.na(databasetaxonomy$g)]
seqinr::write.fasta(sequences = na.omit(databaseselected), file.out = "GutDB.fasta",
names = names(databaseselected), as.string = T)
system(paste(usearch.path, " -makeudb_utax ", "GutDB.fasta", " -output ",
"GutDB.udb", " -taxconfsin ", confidence.file, sep = ""))
} else {
system(paste(usearch.path, " -makeudb_utax ", refDB, " -output ",
"refDB.udb", " -taxconfsin ", confidence.file, sep = ""))
}
}
}
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