Skip to content

Update nextflow.config for improved intrinsic error rate estimation; improved false double codon mutant pre-filtering #62

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
MaximilianStammnitz wants to merge 3 commits into
base: dev
Choose a base branch
from
+86 −2
Open

Update nextflow.config for improved intrinsic error rate estimation; improved false double codon mutant pre-filtering #62

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ab2209e
Update nextflow.config
MaximilianStammnitz Jul 24, 2026
4eddee4
Merge branch 'dev' into dev
MaximilianStammnitz Jul 25, 2026
a5e441f
Update error_correction_false_doubles.R
MaximilianStammnitz Jul 26, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
84 changes: 84 additions & 0 deletions ...cal/dmsanalysis/error_correction_false_doubles/templates/error_correction_false_doubles.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,48 @@ seq_error_correct_by_false_doubles_MLE <- function(wt_path, input_count_path_raw
all.false.doubles <- input.counts.raw
all.false.doubles <- all.false.doubles[which(all.false.doubles[,"varying_bases"] >= 3 & all.false.doubles[,"varying_bases"] < 5 & all.false.doubles[,"varying_codons"] == 2),,drop = F]
all.false.doubles\$codon_dist <- vapply(regmatches(all.false.doubles[,"codon_mut"], gregexpr("\\\\d+(?=:)", all.false.doubles[,"codon_mut"], perl = TRUE)), function(z) abs(diff(as.integer(z))), integer(1))

### additional filters:

#### remove outlier double codon mutants with very high counts
all.false.doubles <- all.false.doubles[which(all.false.doubles\$counts <= quantile(all.false.doubles\$counts, c(0.995))),]

#### only keep 2+1 nt and 3+1 nt double codon mutants
all.false.doubles.nt <- all.false.doubles\$codon_mut
all.false.doubles.nt <- str_split_fixed(all.false.doubles.nt, ", ", 2)
all.false.doubles.nt[,1] <- str_split_fixed(all.false.doubles.nt[,1], ":", 2)[,2]
all.false.doubles.nt[,2] <- str_split_fixed(all.false.doubles.nt[,2], ":", 2)[,2]
classify_double_codon_variant <- function(x) {
parts <- strsplit(x, ">", fixed = TRUE)
n_changes <- vapply(parts, function(p) {
if (length(p) != 2L || nchar(p[1]) != nchar(p[2])) {
return(NA_integer_)
}
sum(strsplit(p[1], "")[[1]] != strsplit(p[2], "")[[1]])
}, integer(1))
labels <- c(1, 2, 3)
ifelse(n_changes %in% 1:3,
labels[n_changes],
ifelse(n_changes == 0L, "no change", NA_character_))
}
all.false.doubles.nt[,1] <- classify_double_codon_variant(all.false.doubles.nt[,1])
all.false.doubles.nt[,2] <- classify_double_codon_variant(all.false.doubles.nt[,2])
if(length(which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2) != 0)){
all.false.doubles <- all.false.doubles[-which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2),]
all.false.doubles.nt <- all.false.doubles.nt[-which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2),]
}
if(length(which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1) != 0)){
all.false.doubles <- all.false.doubles[-which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1),]
all.false.doubles.nt <- all.false.doubles.nt[-which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1),]
}
if(length(which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)) != 0)){
all.false.doubles <- all.false.doubles[-which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)),]
all.false.doubles.nt <- all.false.doubles.nt[-which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)),]
}
if(length(which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T) != 0)){
all.false.doubles <- all.false.doubles[-which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T),]
all.false.doubles.nt <- all.false.doubles.nt[-which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T),]
}

all.false.doubles.codons <- str_split_fixed(all.false.doubles\$codon_mut, ", ", 2)
all.false.doubles.codons[,1] <- as.integer(sub(":.*", "", all.false.doubles.codons[,1]))
Expand Down Expand Up @@ -270,6 +312,48 @@ seq_error_correct_by_false_doubles_EB <- function(wt_path, input_count_path_raw,
all.false.doubles <- input.counts.raw
all.false.doubles <- all.false.doubles[which(all.false.doubles[,"varying_bases"] >= 3 & all.false.doubles[,"varying_bases"] < 5 & all.false.doubles[,"varying_codons"] == 2),,drop = F]
all.false.doubles\$codon_dist <- vapply(regmatches(all.false.doubles[,"codon_mut"], gregexpr("\\\\d+(?=:)", all.false.doubles[,"codon_mut"], perl = TRUE)), function(z) abs(diff(as.integer(z))), integer(1))

### additional filters:

#### remove outlier double codon mutants with very high counts
all.false.doubles <- all.false.doubles[which(all.false.doubles\$counts <= quantile(all.false.doubles\$counts, c(0.995))),]

#### only keep 2+1 nt and 3+1 nt double codon mutants
all.false.doubles.nt <- all.false.doubles\$codon_mut
all.false.doubles.nt <- str_split_fixed(all.false.doubles.nt, ", ", 2)
all.false.doubles.nt[,1] <- str_split_fixed(all.false.doubles.nt[,1], ":", 2)[,2]
all.false.doubles.nt[,2] <- str_split_fixed(all.false.doubles.nt[,2], ":", 2)[,2]
classify_double_codon_variant <- function(x) {
parts <- strsplit(x, ">", fixed = TRUE)
n_changes <- vapply(parts, function(p) {
if (length(p) != 2L || nchar(p[1]) != nchar(p[2])) {
return(NA_integer_)
}
sum(strsplit(p[1], "")[[1]] != strsplit(p[2], "")[[1]])
}, integer(1))
labels <- c(1, 2, 3)
ifelse(n_changes %in% 1:3,
labels[n_changes],
ifelse(n_changes == 0L, "no change", NA_character_))
}
all.false.doubles.nt[,1] <- classify_double_codon_variant(all.false.doubles.nt[,1])
all.false.doubles.nt[,2] <- classify_double_codon_variant(all.false.doubles.nt[,2])
if(length(which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2) != 0)){
all.false.doubles <- all.false.doubles[-which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2),]
all.false.doubles.nt <- all.false.doubles.nt[-which(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 2),]
}
if(length(which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1) != 0)){
all.false.doubles <- all.false.doubles[-which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1),]
all.false.doubles.nt <- all.false.doubles.nt[-which(all.false.doubles.nt[,1] == 1 & all.false.doubles.nt[,2] == 1),]
}
if(length(which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)) != 0)){
all.false.doubles <- all.false.doubles[-which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)),]
all.false.doubles.nt <- all.false.doubles.nt[-which(c(all.false.doubles.nt[,1] == 3 & all.false.doubles.nt[,2] == 2) | c(all.false.doubles.nt[,1] == 2 & all.false.doubles.nt[,2] == 3)),]
}
if(length(which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T) != 0)){
all.false.doubles <- all.false.doubles[-which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T),]
all.false.doubles.nt <- all.false.doubles.nt[-which(is.na(all.false.doubles.nt[,1]) == T | is.na(all.false.doubles.nt[,2]) == T),]
}

all.false.doubles.codons <- str_split_fixed(all.false.doubles\$codon_mut, ", ", 2)
all.false.doubles.codons[,1] <- as.integer(sub(":.*", "", all.false.doubles.codons[,1]))
Expand Down
4 changes: 2 additions & 2 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ params {

input = null

min_counts = 10
base_qual = 30
min_counts = 1
base_qual = 40
min_flank = 2
error_correction = 'false_doubles'
false_doubles_method = 'mle'
Expand Down
Loading