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73 lines
3.8 KiB
Text
73 lines
3.8 KiB
Text
unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
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# Installing missing dependencies
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dependencies <- c("stringi", "progress")
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missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
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if(length(missing_packages)) install.packages(missing_packages)
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# Sanity checks
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check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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check_annotation_sep <- !any(stringi::stri_detect_fixed(str = DATA$AAChange.refGene, pattern = annotation_separator))
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idx_Gene <- which(colnames(DATA) == GeneColName)
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idx_Annotation <- which(colnames(DATA) == AnnotationColName)
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if(length(idx_Gene) == 0 | length(idx_Annotation) == 0 | check_paralog_sep | check_annotation_sep) {
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message(stringi::stri_c("You entered :-->",
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"\nparalog_separator = ",paralog_separator,
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"\nannotation_separator = ",annotation_separator,
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"\nGeneColName = ", GeneColName,
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"\nAnnotationColName = ",AnnotationColName))
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stop("Inconsistencies with these input parameters.\n Ensure they are correct and try again.")
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}
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# Cleanup
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rm(missing_packages,dependencies,check_paralog_sep,check_annotation_sep)
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gc()
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current.idx <- nrow(DATA)+1
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paralog.idx <- which(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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pb <- progress::progress_bar$new(total=length(paralog.idx),format = " [:bar] :current/:total (:percent)",); pb$tick(0)
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Number_of_paralogs <- sum(stringi::stri_count_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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message(stringi::stri_c("There are ",length(paralog.idx)," annotations with ", Number_of_paralogs," paralogs."))
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# copying structure of original DATA
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DATA.add <- DATA[1,]; DATA.add <- DATA.add[-1,]
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# Adding the empty rows to original table.
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# These rows will be populated in the for loop
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DATA.add <- dplyr::bind_rows(DATA.add,data.frame(matrix(nrow = (length(paralog.idx)+Number_of_paralogs), ncol = ncol(DATA),dimnames = list(c(),colnames(DATA))),stringsAsFactors = F))
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DATA <- dplyr::bind_rows(DATA,DATA.add)
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rm(DATA.add) ; gc()
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# Beginning isolation of the paralogs
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for(i in paralog.idx){
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Muts <- unlist(stringi::stri_split_fixed(DATA$AAChange.refGene[i],annotation_separator),use.names = F,recursive = F)
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for (gene in unlist(stringi::stri_split_fixed(DATA$Gene.refGene[i],pattern = paralog_separator),use.names = F,recursive = F)){
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DATA[current.idx,] <- DATA[i,]
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DATA$Gene.refGene[current.idx] <- gene
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DATA$AAChange.refGene[current.idx] <- paste0(Muts[grep(gene,Muts,fixed = T)],collapse=",")
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current.idx <- current.idx+1
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}
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pb$tick(1)
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}
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# removing the original rows with the paralogs as they are all unparalogged now
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DATA <- DATA[-paralog.idx,]
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rownames(DATA) <- as.character(seq(1,length(DATA[,1])))
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return (DATA)
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}
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dependencies <- c("stringi")
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missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
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if(length(missing_packages)) install.packages(missing_packages)
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rm(missing_packages,dependencies)
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MutSiteFind <- function(MutationColumn){
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# #<---------------------------->
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# # Please include this section when distributing and/or using this code.
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# # Please read and abide by the terms of the included LICENSE.
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# # Copyright 2020, Deepankar Chakroborty
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# #
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# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
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# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
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# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
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# #
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# # PURPOSE:
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# # For a given vector of amino acid changes like A123T, V256F, E746_A750del
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# # this function returns c(123, 256, 746) as amino acid positions of
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# # the mutated residue.
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# # In case of indels, it doesn't return the range!! (returns only the start position)
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# #
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# #<---------------------------->
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return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))
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}
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MutSiteFind
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