calling primer3 from R

callPrimer3.R

#' call primer3 for a given set of DNAstringSet object
#'
#' @param seq DNAstring object, one DNA string for the given amplicon
#' @param size_range default: '151-500'
#' @param Tm melting temprature parameters default:c(55,57,58)
#' @param name name of the amplicon in chr_start_end format
#' @param primer3 primer3 location
#' @param therme.param thermodynamic parameters folder
#' @param settings text file for parameters
#' @author Altuna Akalin modified Arnaud Krebs' original function
#' @example
#' 
#' primers=mapply(.callP3NreadOrg,seq=sample.seq,
#'                                   name=names(sample.seq),
#'                      MoreArgs=list(primer3=primer3,size_range=size_range,Tm=Tm,
#'                                    thermo.param=thermoParam,settings=settings)
#'                      ,SIMPLIFY = FALSE)
#' 
#' 
.callP3NreadOrg<-function(seq,size_range='151-500',Tm=c(55,57,58),name,
                       primer3="/work2/gschub/arnaud/softwares/primer3/primer3-2.3.4/bin/primer3_core",
                       thermo.param="/work2/gschub/arnaud/softwares/primer3/primer3-2.3.4/src/primer3_config/",
                       settings="/work2/gschub/arnaud/softwares/primer3/primer3-2.3.4/default_settings.txt"){
  



  #print(excluded.regions)
  # make primer 3 input file
  p3.input=tempfile()
  p3.output=tempfile()
  write(
    paste( sprintf("SEQUENCE_ID=%s\n",name  ),
           sprintf("SEQUENCE_TEMPLATE=%s\n",as.character(seq),
           "PRIMER_TASK=pick_detection_primers\n",
           "PRIMER_PICK_LEFT_PRIMER=1\n" ,
           "PRIMER_PICK_INTERNAL_OLIGO=0\n",
           "PRIMER_PICK_RIGHT_PRIMER=1\n"  ,
           "PRIMER_EXPLAIN_FLAG=1\n"  ,
           "PRIMER_PAIR_MAX_DIFF_TM=3\n",
           sprintf("PRIMER_MIN_TM=%s\n" ,Tm[1]),
           sprintf("PRIMER_OPT_TM=%s\n" ,Tm[2]),
           sprintf("PRIMER_MAX_TM=%s\n" ,Tm[3]),
           sprintf("PRIMER_PRODUCT_SIZE_RANGE=%s\n" ,size_range),
           
           sprintf("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=%s\n" ,thermo.param),
           "=",
           sep=''
    )
    ,
    p3.input
  )
  #call primer 3 and store the output in a temporary file
  
  try(system(
    paste(primer3 ,p3.input, "-p3_settings_file",settings, 
                ">", p3.output)
  ))
  
  #import and parse the output into a dataframe named designed.primers
  out=read.delim(p3.output, sep='=', header=FALSE)
  
  unlink(c(p3.input,p3.output) ) # delete temp files
  returned.primers=as.numeric(as.vector(out[out[,1]=='PRIMER_PAIR_NUM_RETURNED',][,2]))
  if (length(returned.primers)==0){ warning('primers not detected for ',name,call. = FALSE);return(NA)}
  if ((returned.primers)==0){ warning('primers not detected for ',name,call. = FALSE);return(NA)}
  if (returned.primers>0){
    designed.primers=data.frame()
    for (i in seq(0,returned.primers-1,1)){
      #IMPORT SEQUENCES
      id=sprintf(  'PRIMER_LEFT_%i_SEQUENCE',i)
      PRIMER_LEFT_SEQUENCE=as.character(out[out[,1]==id,][,2])
      id=sprintf(  'PRIMER_RIGHT_%i_SEQUENCE',i)
      PRIMER_RIGHT_SEQUENCE=as.character(out[out[,1]==id,][,2])
      
      #IMPORT PRIMING POSITIONS
      id=sprintf(  'PRIMER_LEFT_%i',i)
      PRIMER_LEFT=as.numeric(unlist(strsplit(as.vector((out[out[,1]==id,][,2])),',')))
      #PRIMER_LEFT_LEN=as.numeric(unlist(strsplit(as.vector((out[out[,1]==id,][,2])),',')))
      id=sprintf(  'PRIMER_RIGHT_%i',i)
      PRIMER_RIGHT=as.numeric(unlist(strsplit(as.vector((out[out[,1]==id,][,2])),',')))
      #IMPORT Tm
      id=sprintf(  'PRIMER_LEFT_%i_TM',i)
      PRIMER_LEFT_TM=as.numeric(as.vector((out[out[,1]==id,][,2])),',')
      id=sprintf(  'PRIMER_RIGHT_%i_TM',i)
      PRIMER_RIGHT_TM=as.numeric(as.vector((out[out[,1]==id,][,2])),',')
      
      res=out[grep(i,out[,1]),]
      extra.inf=t(res)[2,,drop=FALSE]
      colnames(extra.inf)=sub( paste("_",i,sep=""),"",res[,1])
      extra.inf=extra.inf[,-c(4:9),drop=FALSE] # remove redundant columns
      extra.inf=apply(extra.inf,2,as.numeric)
      #Aggegate in a dataframe
      primer.info=data.frame(i,
                             PRIMER_LEFT_SEQUENCE,PRIMER_RIGHT_SEQUENCE,
                             PRIMER_LEFT_TM, PRIMER_RIGHT_TM,
                             PRIMER_LEFT_pos=PRIMER_LEFT[1],
                             PRIMER_LEFT_len=PRIMER_LEFT[2], 
                             PRIMER_RIGHT_pos=PRIMER_RIGHT[1], 
                             PRIMER_RIGHT_len=PRIMER_RIGHT[2],
                             t(data.frame(extra.inf))
                             
      )
      rownames(primer.info)=NULL
      designed.primers=rbind(designed.primers, primer.info)
      #print(primer.info)
    }
    
    
    
    #colnames(designed.primers)=c('PrimerID',
    #                             'Fwseq','Rvseq',
    #                             'FwTm','RvTm',
    #                             'FwPos','Fwlen',
    #                             'RvPos','Rvlen',
    #                             'fragLen' )
    
  }
  return(designed.primers)
}


#' convert primer list to genomic intervals
#' 
#' function returns a GRanges or data frame object from a list of primers designed
#' by \code{designPrimers} function after calculating genomic location of the amplicon
#' targeted by the primers.
#' 
#' @param primers a list of primers returned by \code{designPrimers} function
#' @param as.data.frame logical indicating if a data frame should be returned
#'        instead of \code{GRanges} object.
#'        
#' @examples
#'  data(bisPrimers)
#'  # remove data with no primers found
#'  bisPrimers=bisPrimers[!is.na(bisPrimers)]
#'  gr.pr=primers2ranges(bisPrimers) # convert primers to GRanges
#'          
#' @seealso \code{\link{filterPrimers}}, \code{\link{designPrimers}}
#'        
#' @export
#' @docType methods
primers2ranges<-function(primers,as.data.frame=FALSE){
  
  if(any(is.na(primers))){
    warning( "There are targets without primers\nfiltering those before conversion")
    primers=primers[ !is.na(primers) ]
  }
  df=do.call("rbind",primers) # get primers to a df
  locs=gsub("\\|\\.+","",rownames(df)) # get the coordinates from list ids
  temp=do.call("rbind",strsplit(locs,"_")) #
  
  start=as.numeric(temp[,2])
  chr=as.character(temp[,1])
  
  
  
  amp.start= start + as.numeric(df$PRIMER_LEFT_pos)  
  amp.end  = start + as.numeric(df$PRIMER_RIGHT_pos)
  res=data.frame(chr=chr,start=amp.start,end=amp.end,df)
  #saveRDS(res,file="/work2/gschub/altuna/projects/DMR_alignments/all.designed.primers.to.amps.rds")
  if(as.data.frame)
  {
    return(res)
  }
  gr=GRanges(seqnames=res[,1],ranges=IRanges(res[,2],res[,3]) )
  values(gr)=res[,-c(1,2,3)]
  gr
}

To use it do:
library(devtools)
source_url("https://gist.github.com/al2na/8540391/raw/375d1f03226ccf862ed126944c4406824b14d931/callPrimer3.R")

now you can call
.callP3NreadOrg() # calls primer3 for a given DNAstring object
primers2ranges() # converts primer list to GRanges or data.frame

This script looks really useful, I'm keen to try it. However, just to let you know, I am getting this error when I try to source:

Error in source("~/.active-rstudio-document", echo = TRUE) :
~/.active-rstudio-document:54:5: unexpected symbol
53: #call primer 3 and store the output in a temporary file
54: try
^

Hi,

First of all: great functions al2na! They are likely to make my life much easier.

Initially, I got a similar error; I think they come from some unmatched parentheses in the first write() command. I've made some edits in my fork, and now it seems to be working fine. I'm also using it in a repo (https://github.com/nmcglincy/ht-primer-design.git); but I wasn't sure how to link to it from a gist.

Cheers

I think that there is a ) missing in line 51. It should be:
50: ,
51: p3.input)
52: )

Hello,
Superb, it really helped me to write my scripts!
This works well on Linux, but on Windows I have not been able to run primer3 (from R) unless the working directory is set on the primer3 root folder. Trying to call primer3 from elsewhere seems to fail, and pointing at the directories like do in this Linux version does not seem to fix it.
My approach on Windows (since I could not run the rest of my shiny app from the primer3 root folder) was to do a setwd() within the primer3 caller function, and add an on.exit(setwd("myinitialdirectory")) so the working directory is set back to the original one when the function exits.
Cheers,
Ruben

Hi,
Thanks for sharing the code. This could be very useful.

I tried to get the code as indicated in the second post but I get this error message:
Error: could not find function "set_config"

I am new to GitHub, perhaps there are additional packages I need to install or set up a proxy separately.

Did anyone experience anything similar?

Best,
Massimo