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Merge pull request #3 from loosolab/cluster
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Cluster
renewiegandt committed Dec 6, 2018
2 parents 2700ce7 + 92baa4d commit 8274bc3
Showing 4 changed files with 180 additions and 51 deletions.
119 changes: 101 additions & 18 deletions bin/cdhit_wrapper.R
Original file line number Diff line number Diff line change
@@ -2,50 +2,133 @@
library("optparse")

option_list <- list(
make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Last column must be sequences.", metavar = "character"),
make_option(opt_str = c("-s", "--similarity"), default = 0.8, help = "Similarity threshold. Default = %default", metavar = "double >= 0.8"),
make_option(opt_str = c("-A", "--coverage"), default = 8, help = "Minimal alignment length for both sequences in nucelotides. Default = %default", metavar = "integer"),
make_option(opt_str = c("-o", "--output"), default = "cluster.bed", help = "Output file. Default = %default", metavar = "character"),
make_option(opt_str = c("-c", "--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical")
# TODO more args
make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Fourth column is expected to contain names, last column must be sequences.", metavar = "character"),
make_option(opt_str = c("-c", "--identity"), default = 0.8, help = "Identity threshold. Default = %default (CD-HIT parameter)", metavar = "double >= 0.8"),
make_option(opt_str = c("-A", "--coverage"), default = 8, help = "Minimal alignment length for both sequences in nucelotides. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-o", "--output"), default = "cluster.bed", help = "Output file same as input but with appended column of cluster numbers. Default = %default", metavar = "character"),
make_option(opt_str = c("--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical"),
make_option(opt_str = c("-G", "--global"), default = 0, help = "Global sequence identity = 1, local = 0. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-b", "--band_width"), default = 20, help = "Alignment band width. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-M", "--memory"), default = 800, help = "Memory limit in MB. 0 for unlimited. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-T", "--threads"), default = 1, help = "Number of threads. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-n", "--word_length"), default = 3, help = "Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-l", "--throw_away_sequences"), default = 5, help = "Maximum length of sequences thrown away. Default = %default (CD-HIT parameter)", metavar = "integer"),
# make_option(opt_str = c("-d", "--description")), # can not produce bed if this is != 0
make_option(opt_str = c("-s", "--length_dif_cutoff_shorter_p"), default = 0.0, help = "Shorter sequences length must be at least x percent of longer sequenecs length. Default = %default (CD-HIT parameter)", metavar = "double"),
make_option(opt_str = c("-S", "--length_dif_cutoff_shorter_n"), default = 999999, help = "Length difference between sequences can not be higher than x nucleotides. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-e", "--alignment_coverage_longer_p"), default = 0.0, help = "Alignment must cover x percent of longer sequence. Default = %default (CD-HIT parameter: -aL)", metavar = "double"),
make_option(opt_str = c("-E", "--alignment_coverage_longer_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter: -AL)", metavar = "integer"),
make_option(opt_str = c("-f", "--alignment_coverage_shorter_p"), default = 0.0, help = "Alignment must cover x percent of shorter sequence. Default = %default (CD-HIT parameter: -aS)", metavar = "double"),
make_option(opt_str = c("-F", "--alignment_coverage_shorter_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter: -AS)", metavar = "integer"),
make_option(opt_str = c("-w", "--max_unmatched_longer_p"), default = 1.0, help = "Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uL)", metavar = "double"),
make_option(opt_str = c("-W", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uS)", metavar = "double"),
make_option(opt_str = c("-U", "--max_unmatched_both_n"), default = 99999999, help = "Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-g", "--fast_cluster"), default = 1, help = "Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-r", "--strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("--match"), default = 2, help = "Matching score. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("--mismatch"), default = -2, help = "Mismatch score. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("--gap"), default = -6, help = "Gap score. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("--gap_ext"), default = -1, help = "Gap extension score. Default = %default (CD-HIT parameter)", metavar = "integer"),
make_option(opt_str = c("-x", "--sort_cluster_by_size"), default = 1, help = "Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = %default (CD-HIT parameter: -sc)", metavar = "integer")
)

opt_parser <- OptionParser(option_list = option_list,
description = "CD-HIT-EST Wrapper function.")
description = "CD-HIT-EST Wrapper function. See https://github.com/weizhongli/cdhit/wiki for more information regarding CD-HITs parameters.")

opt <- parse_args(opt_parser)

#' cd-hit wrapper
#' cd-hit-est wrapper
#' Receives bed with sequences in last column and writes bed with added cluster numbers.
#'
#' @param input
#' @param similarity Similarity threshold.
#' @param coverage Minimal alignment length for both sequences in nucelotides.
#' @param output Clustered bedfile. Adds cluster number in last column (lower number = bigger cluster).
#' @param clean Clean up after run.
#' @param input Data.table or file in bed format (requires names in fourth column and sequences in last column).
#' @param identity Identity threshold. Default = 0.8 (CD-HIT parameter)
#' @param coverage Minimal alignment length for both sequences in nucelotides. Default = 8 (CD-HIT parameter)
#' @param output Clustered bedfile. Adds cluster number in last column (numbering depend on sort_by_cluster_size parameter). Default = cluster.bed
#' @param clean Clean up after run. Default = TRUE
#' @param threads Number of threads to use (0 = all cores). Default = 1 (CD-HIT parameter)
#' @param global Global sequence identity = 1, local = 0. Default = 0 (CD-HIT parameter)
#' @param band_width "Alignment band width. Default = 20 (CD-HIT parameter)"
#' @param memory Memory limit in MB. 0 for unlimited. Default = 800 (CD-HIT parameter)
#' @param word_length Default = 3 (CD-HIT parameter)
#' @param throw_away_sequences Maximum length of sequences thrown away. Default = %default (CD-HIT parameter)
#' @param length_dif_cutoff_shorter_p Shorter sequences length must be at least x percent of longer sequenecs length. Default = 0 (CD-HIT parameter)
#' @param length_dif_cutoff_shorter_n Length difference between sequences can not be higher than x nucleotides. Default = 999999 (CD-HIT parameter)
#' @param alignment_coverage_longer_p Alignment must cover x percent of longer sequence. Default = 0 (CD-HIT parameter)
#' @param alignment_coverage_longer_n There can not be more than x unaligned nucleotides on the longer sequence. Default = 99999999 (CD-HIT parameter)
#' @param alignment_coverage_shorter_p Alignment must cover x percent of shorter sequence. Default = 0 (CD-HIT parameter)
#' @param alignment_coverage_shorter_n There can not be more than x unaligned nucleotides on the longer sequence. Default = 99999999 (CD-HIT parameter)
#' @param max_unmatched_longer_p Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = 1 (CD-HIT parameter)
#' @param max_unmatched_shorter_p Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = 1 (CD-HIT parameter)
#' @param max_unmatched_both_n Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = 99999999 (CD-HIT parameter)
#' @param fast_cluster Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = 1 (CD-HIT parameter)
#' @param strand Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = 0 (CD-HIT parameter)
#' @param match Matching score. Default = 2 (CD-HIT parameter)
#' @param mismatch Mismatch score. Default = -2 (CD-HIT parameter)
#' @param gap Gap score. Default = -6 (CD-HIT parameter)
#' @param gat_ext Gap extension score. Default = -1 (CD-HIT parameter)
#' @param sort_cluster_by_size Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = 1 (CD-HIT parameter)
#'
#' @return bed_table with cluster in last column
#' TODO add all cdhit parameter
#' TODO check whether cdhit is installed
cdhitest <- function(input, similarity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE) {
cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE, threads = 1, global = 0, band_width = 20, memory = 800, word_length = 3, throw_away_sequences = 5, length_dif_cutoff_shorter_p = 0, length_dif_cutoff_shorter_n = 999999, alignment_coverage_longer_p = 0, alignment_coverage_longer_n = 99999999, alignment_coverage_shorter_p = 0, alignment_coverage_shorter_n = 99999999, max_unmatched_longer_p = 1, max_unmatched_shorter_p = 1, max_unmatched_both_n = 99999999, fast_cluster = 1, strand = 0, match = 2, mismatch = -2, gap = -6, gap_ext = -1, sort_cluster_by_size = 1) {
if (missing(input)) {
stop("Input parameter missing!")
}

message("Loading bed.")
# load bed if neccessary
if (!data.table::is.data.table(input)) {
bed_table <- data.table::fread(input = input, header = FALSE)
} else {
bed_table <- input
}

# check for duplicated names
if (anyDuplicated(bed_table[, "V4"])) {
warning("Found duplicated names. Making names unique.")
bed_table[, V4 := make.unique(V4)]
}

message("Convert to fasta.")
### convert bed to fasta
# 4th column = name
# last column = sequence
fasta_file <- "converted_bed.fasta"
seqinr::write.fasta(sequences = as.list(bed_table[[ncol(bed_table)]]), names = bed_table[[4]], as.string = TRUE, file.out = fasta_file)

message("Clustering.")
### cd-hit-est
cdhit_output <- "cdhit_output"
cdhit_call <- paste("cd-hit-est -i", fasta_file, "-o", cdhit_output, "-c", similarity, "-A", coverage, "-G 0 -n 3 -g 1 -r 0 -l 5 -sc 1 -d 0")
cdhit_call <- paste("cd-hit-est -i", fasta_file,
"-o", cdhit_output,
"-c", identity,
"-A", coverage,
"-T", threads,
"-G", global,
"-b", band_width,
"-M", memory,
"-n", word_length,
"-l", throw_away_sequences,
"-s", length_dif_cutoff_shorter_p,
"-S", length_dif_cutoff_shorter_n,
"-aL", alignment_coverage_longer_p,
"-AL", alignment_coverage_longer_n,
"-aS", alignment_coverage_shorter_p,
"-AS", alignment_coverage_shorter_n,
"-uL", max_unmatched_longer_p,
"-uS", max_unmatched_shorter_p,
"-U", max_unmatched_both_n,
"-g", fast_cluster,
"-r", strand,
"-match", match,
"-mismatch", mismatch,
"-gap", gap,
"-gap-ext", gap_ext,
"-sc", sort_cluster_by_size,
"-d 0")

system(command = cdhit_call, wait = TRUE)

message("Formatting/ writing results.")
# reformat cluster file
# columns: id, clstr, clstr_size, length, clstr_rep, clstr_iden, clstr_cov
cluster_file <- "reformated.clstr"
@@ -71,5 +154,5 @@ cdhitest <- function(input, similarity = 0.8, coverage = 8, output = "cluster.be
if (!interactive()) {
# remove last parameter (help param)
params <- opt[-length(opt)]
do.call(cdhitest, args = params)
do.call(cdhitest, args = params)
}

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