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4_Annotate_NoPAM.R
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4_Annotate_NoPAM.R
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########################
#
#Exon 20
#
##################################
setwd("/data/CCBR/rawdata/nousome/1046/Exon20/x20_annotate/CRISPRAnnotation")
source("0_FXN_update.R")
pacman::p_load("biomaRt")
getGeneInfo("BRCA2")
d1=Sys.glob("../CRISPResso*")
dout=sapply(strsplit(basename(d1),"_"),'[',6)
###Add dupliate statement
dout=make.unique(dout)
c1=sprintf('./CRISPR_Annotate.sh -i "%s/%s" -g BRCA2 -s 0 -e 0 -p 0 -a A -o %s',
dirname(getwd()),basename(d1),dout)
write.table(c1,"all.sh",row.names=F,quote=F,col.names=F)
sapply(c1,system)
#####After annotation rerun with the updated codes
pacman::p_load(tidyverse,biomaRt,Biostrings,GenomicRanges,httr,readxl)
source("0_FXN_update.R")
opt=list()
opt$gene="BRCA2"
files=sub(".rds","",sub("afch_","",Sys.glob("afch*.rds")))
getGeneInfo(opt$gene)
##Add filter to the location to
####Process all inital reads to calculate the N
process_output=function(filein){
print(filein)
af_file=readRDS(sprintf("afch_%s.rds",filein))
vt_file=readRDS(sprintf("vt_full_%s.rds",filein))
newdt=left_join(af_file[[1]],vt_file[[1]],by="af.id") %>%
group_by(af.id) %>%
mutate(true_n_del=max(str_count(Aligned,"-"),sum(ALT=="-")),
true_n_ins=max(str_count(Reference,"-"),sum(REF=="-")),
true_n_mutated=sum(ALT %in% c("A","T","G","C","N"))) %>%
ungroup() %>%
relocate(Aligned,.after=ALT) %>%
relocate(Reference,.after=Aligned) %>% distinct()
##Function for creating new
out=list()
newdt1=newdt %>%
filter(n_mutated==1 & n_deleted==0 & n_inserted==0)
out[[1]]=newdt1 %>%
dplyr::select(Reference,Aligned,AAChange.refGene,Reads_n,Reads_prop,REF,ALT,everything())
newdt1=newdt %>%
filter(true_n_mutated==1 & true_n_del==0 & true_n_ins==0)
out[[2]]=newdt1 %>%
dplyr::select(Reference,Aligned,AAChange.refGene,Reads_n,Reads_prop,REF,ALT,everything())
return(out)
}
out_final=lapply(files,process_output)
names(out_final)=files
#names(out_final1)=files
openxlsx::write.xlsx(sapply(out_final,'[',2),sprintf("Annotated_filtered_%s_%s.xlsx",basename(dirname(getwd())),"Exon20"),overwrite=T)
##Try to split PAIRS by CIS/HAT,M15,OLA if they exists
pairs=lapply(c("(?i)CIS","(?i)HAT","(?i)M15","(?i)OLA"),function(x){
grep(x,names(out_final),value=T)
})
names(pairs)=c("CIS","HAT","M15","OLA")
##Pivot FXN
pivot_all=function(pairs,inputfile){
lapply(pairs,function(x){
all_in=lapply(x,function(z){
read_xlsx(inputfile,sheet=z)
})
names(all_in)=x
all_in %>% bind_rows(.,.id = "id" ) %>% dplyr::select(-af.id) %>% #distinct() %>%
#select(-Reference,-Aligned,-AAChange.refGene) %>%
pivot_longer(cols=c(Reads_n,Reads_prop)) %>%
pivot_wider(#id_cols = c(REF,ALT,chr,Start,End),
names_from=c(id,name),values_from=value) %>%
dplyr::select(REF,ALT,everything())
})
}
inputfile=sprintf("Annotated_filtered_%s_%s.xlsx",basename(dirname(getwd())),"Exon20")
out1=pivot_all(pairs,inputfile)
names(out1)=names(pairs)
openxlsx::write.xlsx(out1,sprintf("Annotated_bygroup_%s_%s.xlsx",basename(dirname(getwd())),"Exon20"),overwrite=T)
##Final Combination
final_combined=lapply(excel_sheets(sprintf("Annotated_bygroup_%s_%s.xlsx",basename(dirname(getwd())),"Exon20")),function(x){
read_xlsx(sprintf("Annotated_bygroup_%s_%s.xlsx",basename(dirname(getwd())),"Exon20"),x)
}) %>% purrr::reduce(full_join, by = c('REF','ALT','Reference','Aligned','AAChange.refGene','n_deleted','n_inserted','n_mutated','chr',
'Start','End','Func.refGene','Gene.refGene','gnomad','gnomad_non_topmed','gnomad_female','gnomad_noncancer',
'SIFT_score','Polyphen2_HDIV_score','Polyphen2_HVAR_score','CADD_raw','phyloP30way_mammalian','CLNSIG','true_n_del',
'true_n_ins','true_n_mutated')) %>% arrange(Start,REF)
openxlsx::write.xlsx(final_combined,sprintf("Annotated_combined_%s_%s.xlsx",basename(dirname(getwd())),"Exon20"),overwrite=T)
##ORiginal
out_final=lapply(files,function(z){
print(z)
af_file=readRDS(sprintf("afch_%s.rds",z))
vt_file=readRDS(sprintf("vt_full_%s.rds",z))
##Filter out the vt file since there are a
temp=vt_file[[1]] #%>% filter(chr==13,Start>=32376646,End<=32376816)
newdt=left_join(af_file[[1]],temp,by="af.id") %>%
group_by(af.id) %>%
mutate(true_n_del=max(str_count(Aligned,"-"),sum(ALT=="-")),
#true_n_ins=max(str_count(Reference,"-"),sum(REF=="-")),
true_n_mutated=sum(ALT %in% c("A","T","G","C","N"))) %>%
ungroup() %>%
relocate(Aligned,.after=ALT) %>%
relocate(Reference,.after=Aligned) %>% distinct()
##Function for creating new ref seq
newdt1=newdt %>%
filter(n_mutated==1 & n_deleted==0 & n_inserted==0)
newdt1 %>% dplyr::select(Reference,Aligned,AAChange.refGene,Reads_n,Reads_prop
,REF,ALT,everything())
})
out_final1=lapply(files,function(z){
print(z)
af_file=readRDS(sprintf("afch_%s.rds",z))
vt_file=readRDS(sprintf("vt_full_%s.rds",z))
temp=vt_file[[1]] %>% filter(chr==13,Start>=32376646,End<=32376816)
newdt=left_join(af_file[[1]],temp,by="af.id") %>%
group_by(af.id) %>%
mutate(true_n_del=max(str_count(Aligned,"-"),sum(ALT=="-")),
# true_n_ins=max(str_count(Reference,"-"),sum(REF=="-")),
true_n_mutated=sum(ALT %in% c("A","T","G","C","N"))) %>%
ungroup() %>%
relocate(Aligned,.after=ALT) %>%
relocate(Reference,.after=Aligned) %>% distinct()
newdt1=newdt %>%
filter(true_n_mutated==1 & true_n_del==0)
newdt1 %>% dplyr::select(Reference,Aligned,AAChange.refGene,Reads_n,Reads_prop
,REF,ALT,everything())
})
sapply(out_final,nrow)
sapply(out_final1,nrow)
names(out_final)=files
names(out_final1)=files
openxlsx::write.xlsx(out_final,sprintf("Annotated_Exon21.xlsx"),overwrite=T)
openxlsx::write.xlsx(out_final1,sprintf("Annotated_filtered_%s.xlsx",opt$out),overwrite=T)
openxlsx::write.xlsx(out_final,sprintf("Annotated_Exon21_test.xlsx"),overwrite=T)
openxlsx::write.xlsx(out_final1,sprintf("Annotated_filtered_%s_test.xlsx","Exon21"),overwrite=T)
##Try to split PAIRS by CIS/HAT,M15,OLA if they exists
pairs=lapply(c("(?i)CIS","(?i)HAT","(?i)M15","(?i)OLA"),function(x){
grep(x,names(out_final),value=T)
})
names(pairs)=c("CIS","HAT","M15","OLA")
out1=lapply(pairs[[3]],function(x){
all_in=lapply(x,function(z){
read_xlsx("Annotated_filtered_Exon21_test.xlsx",sheet=z,
col_types=c('text','text','text','numeric','numeric',
'text','text',
'numeric','numeric','numeric','numeric','numeric','numeric','numeric',
'text','text','numeric','numeric','numeric',
'numeric','numeric','numeric','numeric','numeric','numeric',
'text','numeric','numeric'))
})
names(all_in)=x
all_in2=lapply(all_in,function(x){
filter(x,!is.na(REF),!is.na(ALT))
})
#all_in1=lapply(all_in,function(x)
# classes(x)class)
all_in2 %>% bind_rows(.,.id = "id" ) %>% dplyr::select(-af.id) %>% #distinct() %>%
#select(-Reference,-Aligned,-AAChange.refGene) %>%
pivot_longer(cols=c(Reads_n,Reads_prop)) %>%
pivot_wider(#id_cols = c(REF,ALT,chr,Start,End),
names_from=c(id,name),values_from=value) %>%
dplyr::select(REF,ALT,everything()) #%>%
#filter(if_all(ends_with("Reads_prop"),~.>0.002))
})
names(out1)=c("M15","HAT","Cis","Ola")
openxlsx::write.xlsx(out1,"Annotated_filtered_bygroup_Exon21_test.xlsx",overwrite=T)