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0_FXN_update.R
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########All Support Functions
#Process Allele frequency_table--Output as a dataframe with only the Aligned Sequences
allele_freq_tab=function(file,file_ext){
##Xlsx/txt will return list length 1
if(file_ext=="xlsx"){
sheets=readxl::excel_sheets(file)
out_tab=lapply(sheets,function(x){
mytable=readxl::read_xlsx(file,sheet = x)
this <- mytable %>%
dplyr::select(Aligned_Sequence,
Reference_Sequence,
n_deleted,n_inserted,n_mutated,Reads_n=`#Reads`,Reads_prop=`%Reads`) %>%
filter(n_mutated > 0)
# split(this,1:nrow(this))
})
names(out_tab)=sheets
return(out_tab)
}else if(file_ext=="txt"){
mytable = vroom::vroom(x)
this <- mytable %>%
dplyr::select(Aligned_Sequence,
Reference_Sequence,
n_deleted,n_inserted,n_mutated,Reads_n=`#Reads`,Reads_prop=`%Reads`) %>%
filter(n_mutated > 0)
# out_tab=split(this,1:nrow(this))
return(mytable)
}else {
##Filter on only those that have any number of mutations
crispresso_file_name="Alleles_frequency_table.zip"
myfiles = list.files(path=file, pattern = crispresso_file_name, recursive = T, full.names = T)
myfiles.txt=sub(".zip",".txt",myfiles)
names(myfiles) = gsub("^CRISPResso_on_","",basename(dirname(myfiles)))
if(file.info(myfiles)$size>50000000){
system(sprintf("unzip -o %s -d %s",myfiles,dirname(myfiles)))
out_tab=lapply(myfiles.txt,function(x){
mytable=vroom::vroom(x)
this <- mytable %>%
dplyr::select(Aligned_Sequence,
Reference_Sequence,
n_deleted,n_inserted,n_mutated,Reads_n=`#Reads`,Reads_prop=`%Reads`) %>%
filter(n_mutated > 0)
})
names(out_tab)=names(myfiles)
}else{
out_tab=lapply(myfiles,function(x){
mytable=vroom::vroom(unz(x,"Alleles_frequency_table.txt"))
this <- mytable %>%
dplyr::select(Aligned_Sequence,
Reference_Sequence,
n_deleted,n_inserted,n_mutated,Reads_n=`#Reads`,Reads_prop=`%Reads`) %>%
filter(n_mutated > 0)
})
names(out_tab)=names(myfiles)
}
return(out_tab)
}
}
align_crispresso=function(Aligned_Sequence,Reference_Sequence,n_deleted,n_inserted,n_mutated,Reads_n,Reads_prop){
##Run Alignment
alignment=pairwiseAlignment(DNAString(Aligned_Sequence),DNAString(gene_sequence),type="global-local")
##View Alignment
#seq <- c(alignedPattern(alignment), alignedSubject(alignment))
#DECIPHER::BrowseSeqs(seq)
mmt=mismatchTable(alignment)
##INDELS FIRST TO ADD TO TABLE
indT=indel(alignment)
ins=data.frame(indT@insertion@unlistData)
del=data.frame(indT@deletion@unlistData)
vt_snp=tibble(chr=gene_coords$chr,Start=gene_coords$start+mmt$SubjectStart-1,
End=gene_coords$start+mmt$SubjectEnd-1,
REF=mmt$SubjectSubstring,ALT=mmt$PatternSubstring,
Aligned=Aligned_Sequence,Reference=Reference_Sequence,
n_deleted=n_deleted,n_inserted=n_inserted,n_mutated=n_mutated,
Reads_n=Reads_n,Reads_prop=Reads_prop)
if(nrow(ins)>0){
##INSERTION REF
shift <- c(0L, head(cumsum(width(indT@insertion)[[1]]), n=-1L))
ins_ranges <- shift(indT@insertion[[1]], shift)
# end(ins_ranges)=ifelse(end(ins_ranges)>end(alignment@pattern@range),end(alignment@pattern@range),end(ins_ranges))
#ins_seqs <- extractAt(alignment@pattern@unaligned[[1]], ins_ranges)
aligned_pattern <- as(as.character(pattern(alignment)),
paste0(seqtype(pattern(alignment)), "String"))
ins_seqs <- extractAt(aligned_pattern, ins_ranges)
ins_seqs_dt=data.frame(ins_seqs@ranges)
ins_alt=data.frame(ins_seqs)
vt_ins=tibble(chr=gene_coords$chr,
Start=(gene_coords$start+alignment@subject@range@start+ins$start)-3,
End=gene_coords$start+ins$start+alignment@subject@range@start+ins$width-3,
REF="-",ALT=ins_alt$ins_seqs,
Aligned=Aligned_Sequence,Reference=Reference_Sequence,
n_deleted=n_deleted,n_inserted=n_inserted,n_mutated=n_mutated,
Reads_n=Reads_n,Reads_prop=Reads_prop)
}
if(nrow(del)>0){
shift <- c(0L, head(cumsum(width(indT@deletion[[1]])), n=-1L))
del_ranges <- shift(indT@deletion[[1]], shift)
aligned_subject <- as(as.character(alignment@subject),
paste0(seqtype(subject(alignment)), "String"))
del_seqs <- extractAt(aligned_subject, del_ranges)
#end(del_ranges)=ifelse(end(del_ranges)>end(d@subject@range),end(d@pattern@range),end(del_ranges))
#del_ranges=data.frame(start=del_ranges@start-sum(ins$width),end=del_ranges@start-sum(ins$width)+del_ranges@width)
del_ranges=data.frame(del_seqs@ranges)
#del_alt=data.frame(del_seqs)
vt_del=tibble(chr=gene_coords$chr,
Start=(gene_coords$start+alignment@subject@range@start+del_ranges$start)-2,
End=(gene_coords$start+alignment@subject@range@start+del_ranges$end)-2,
REF=data.frame(del_seqs)$del_seqs,ALT="-",
Aligned=Aligned_Sequence,Reference=Reference_Sequence,
n_deleted=n_deleted,n_inserted=n_inserted,n_mutated=n_mutated,
Reads_n=Reads_n,Reads_prop=Reads_prop)
}
if(exists("vt_del") & exists("vt_ins")){
bind_rows(vt_del,vt_ins,vt_snp) %>% arrange(Start)
}else if(exists("vt_ins")){
bind_rows(vt_ins,vt_snp) %>% arrange(Start)
}else if(exists("vt_del")){
bind_rows(vt_del,vt_snp) %>% arrange(Start)
}else{
vt_snp %>% arrange(Start)
}
}
aachange=function(POS,dt){
REFnt=sapply(POS-gene_coords$start+1,function(x)as.character(subseq(DNAString(gene_sequence),x,x)))
REFdt=data.frame(REF=REFnt,POS=POS) %>%
left_join(.,dt,by=c("REF",c("POS"="Start")))
newalt=ifelse(is.na(REFdt$ALT),REFdt$REF,REFdt$ALT)
newref=paste(REFnt,collapse="")
data.frame(REFnt=newref,ALTnt=paste(newalt,collapse=""),REF=as.character(translate(DNAString(newref))),ALT=as.character(translate(DNAString(paste(newalt,collapse="")))))
}
getGeneInfo=function(genename){
##Load the Gene Name into the name space right away!
if(file.exists(sprintf("%s_gene_coords.rds",genename)) & file.exists(sprintf("%s_gene_sequence.rds",genename))){
assign('gene_coords',readRDS(sprintf("%s_gene_coords.rds",genename)),envir =globalenv())
assign('gene_sequence',readRDS(sprintf("%s_gene_sequence.rds",genename)),envir = globalenv())
}else{
mart = useMart('ensembl', dataset="hsapiens_gene_ensembl")
#mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "asia.ensembl.org")
my_attrs = c(gene="external_gene_name",chr="chromosome_name",start="start_position",
end="end_position",strand="strand",sequence="gene_exon_intron")
gene_sequence_info = getBM(attributes = my_attrs,
filters = "external_gene_name",
values = genename, mart = mart, verbose=T)
gene_sequence_info = gene_sequence_info[,match(my_attrs, colnames(gene_sequence_info))]
colnames(gene_sequence_info) = names(my_attrs)
gene_coords = gene_sequence_info[gene_sequence_info$gene==genename,
c("chr","start","end","strand")]
gene_sequence = gene_sequence_info$sequence[gene_sequence_info$gene==genename]
saveRDS(gene_coords,sprintf("%s_gene_coords.rds",genename))
saveRDS(gene_sequence,sprintf("%s_gene_sequence.rds",genename))
assign('gene_coords',readRDS(sprintf("%s_gene_coords.rds",genename)),envir =globalenv())
assign('gene_sequence',readRDS(sprintf("%s_gene_sequence.rds",genename)),envir = globalenv())
}
}
##Return AA annotation
return_AA_anno=function(split_dataframe,positions,annotin){
lapply(split_dataframe,function(x){
POS=positions
AA1_change=aachange(POS,dt=x)
reg_ex=paste0(gene_coords$chr[1],":",POS[1],"-",POS[3])
tempa=annotin %>% filter(X2 %in% reg_ex) %>% dplyr::select(X3,REF_AA,ALT_AA,SIFT,Polyphen,CADD)
data.frame(af.id=x$af.id[1],AA1_change) %>% left_join(.,tempa,by=c('REF'='REF_AA','ALT'="ALT_AA",'ALTnt'="X3"))%>%
dplyr::rename(REF_AA=REF,ALT_AA=ALT,SIFT_AA=SIFT,Polyphen_AA=Polyphen,CADD_AA=CADD)
})
}