R/kneaddata.R

In seedpcseed/momics2:

#kneaddata scripts
#
#
#required are:
# kneaddata_database --download human_genome bowtie2 $DIR
# kneaddata_database --download ribosomal_RNA bowtie2 $DIR
#
# trimmomatic
# bowtie2
#
# may be required are:
# kneaddata_database --download human_transcriptome bowtie2 $DIR
# kneaddata_database --download mouse_C57BL bowtie2 $DIR
#
#
# reference sequences need to be indexed (the downloads are for bowtie2)
#
#

kneadData_single<- function(
  INPUT_FOLDER,
  REFERENCE_DB=KNEADDATA_DB_HUMAN,
  OUTPUT="kneaddata",
  PATTERN="*.fastq.gz"
){
  OUTPUT=file.path(getwd(), OUTPUT)
  if(!dir.exists(OUTPUT)){system(paste0("mkdir ", OUTPUT))}
  for(i in list.files(INPUT_FOLDER, pattern=PATTERN, include.dirs=TRUE, full.names = TRUE)){
    code=paste0("kneaddata --input ", i, " --reference-db ",
                REFERENCE_DB, " --output ", OUTPUT)
    if(SINGULARITY){
      code=paste0("singularity exec -B ", SINGULARITY_B, " ", SINGULARITY_IMAGE, " ", code)
    }
    system(code)
  }
}

kneadData_paired<-function(
  INPUT_FOLDER,
  REFERENCE_DB=KNEADDATA_DB_HUMAN,
  OUTPUT="kneaddata",
  PATTERN1="R1",
  PATTERN2="R2",
  ADD_ON=" --cat-final-output "
){
  INPUT_FOLDER=file.path(getwd(), INPUT_FOLDER)
  q<-sprintf("INPUT_FOLDER= %s", INPUT_FOLDER)
  print(q)
  OUTPUT=file.path(getwd(), OUTPUT)
  q<-sprintf("OUTPUT= %s", OUTPUT)
  print(q)
  if(!dir.exists(OUTPUT)){system(paste0("mkdir ", OUTPUT))}

  q<- sprintf("PATTERN1: %s and PATTERN2: %s", PATTERN1, PATTERN2)
  print(q)

  R1=list.files(INPUT_FOLDER, pattern=PATTERN1, include.dirs=TRUE, full.names = TRUE)
  R2=list.files(INPUT_FOLDER, pattern=PATTERN2, include.dirs=TRUE, full.names = TRUE)

  R1<-sort(R1)
  q<-sprintf("R1 FILES: %s", R1); print(q)

  R2<-sort(R2)
  q<-sprintf("R2 FILES: %s", R2); print(q)

  for(i in 1:length(R1)){
    code=paste0("kneaddata --input ", R1[i], " --input ", R2[i], " --reference-db ",
                REFERENCE_DB, " --output ", OUTPUT, " ", ADD_ON)
    if(SINGULARITY){
      code=paste0("singularity exec -B ", SINGULARITY_B, " ", SINGULARITY_IMAGE, " ", code)
    }
    q<-sprintf("Code: %s", code)
    print(q)
    system(code)
  }
}

kneadData_cat<-function(
  INPUT_FOLDERS,
  OUTPUT_FOLDER
){  #for nextseq where the files are all split apart

}

kneadData_gather<- function(){ #where the sequencing files are separated in different folders

}