comparison single_fastq_filtering.R @ 5:378565f5a875 draft

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4:d397f5a85464

cat("number of sequences in ",opt$fastqA,":",n1,"\n")
cat("--------\n")


number_of_chunks=round(n1/CHUNK_SIZE)
if (number_of_chunks==0){
	CHUNK_SIZE=n1
	number_of_chunks=1
}
if (!is.null(opt$sample_size)){
	sample_size_in_chunk=opt$sample_size/number_of_chunks
}else{
	sample_size_in_chunk=CHUNK_SIZE
}

# adjust the chunk size to get exact count of sequences:
CHUNK_SIZE = ceiling(n1/number_of_chunks)
save.image("tmp.RData")

print("--------------------------------")
print (sample_size_in_chunk)
print (opt$sample_size)
print (CHUNK_SIZE)
print("--------------------------------")
f1 <- FastqStreamer(opt$fastqA, CHUNK_SIZE)
total=0
nucleotideFrequenciesForward = matrix(0)
while(TRUE){
	print (Sys.time())

  

	# filter complete pairs again:

	# create new id - last character must differentiate pair - for interlacig
	if (length(fqF1)>sample_size_in_chunk){
		smp=sort(sample(seq_along(fqF1),sample_size_in_chunk))
		writeFun(fqF1[smp],file=f1out,mode='a')
    nfrq1 = alphabetByCycle(sread(fqF1[smp]))

	}else{
      writeFun(fqF1,file=f1out,mode='a')

5:378565f5a875

cat("number of sequences in ",opt$fastqA,":",n1,"\n")
cat("--------\n")


number_of_chunks=round(n1/CHUNK_SIZE)
CHUNK_SIZE = round(n1/number_of_chunks)

if (number_of_chunks==0){
	CHUNK_SIZE=n1
	number_of_chunks=1
}
if (!is.null(opt$sample_size)){
	sample_size_in_chunk=round(opt$sample_size/number_of_chunks)
  n_missing = opt$sample_size - sample_size_in_chunk * number_of_chunks
}else{
	sample_size_in_chunk=CHUNK_SIZE
  n_missing = 0
}

# adjust the chunk size to get exact count of sequences:
CHUNK_SIZE = ceiling(n1/number_of_chunks)
save.image("tmp.RData")


f1 <- FastqStreamer(opt$fastqA, CHUNK_SIZE)
total=0
nucleotideFrequenciesForward = matrix(0)
while(TRUE){
	print (Sys.time())

  

	# filter complete pairs again:

	# create new id - last character must differentiate pair - for interlacig
	if (length(fqF1)>(sample_size_in_chunk + n_missing)){
		smp=sort(sample(seq_along(fqF1),sample_size_in_chunk + n_missing))
    n_missing = 0
		writeFun(fqF1[smp],file=f1out,mode='a')
    nfrq1 = alphabetByCycle(sread(fqF1[smp]))

	}else{
      writeFun(fqF1,file=f1out,mode='a')