write_reads: write sequencing reads to disk
In alyssafrazee/polyester: Simulate RNA-seq reads

Description Usage Arguments Details Value See Also Examples

given a DNAStringSet representing simulated sequencing reads, write FASTA files to disk representing the simulated reads.

1	write_reads(reads, fname, readlen, paired = TRUE, gzip, offset = 1L)

`reads`	DNAStringSet representing sequencing reads
`fname`	file path/prefix specifying where sequencing reads should be written. Should not contain ".fasta" (this is appended automatically).
`readlen`	maximum length of the reads in `reads`.
`paired`	If `TRUE`, reads are assumed to be in pairs: i.e., read 1 and read 2 in `reads` are the left and right mate (respectively) of a read pair; same with read 3 and read 4, etc. The odd-numbered reads are written to `fname_1.fasta` and the even-numbered reads are written to `fname_2.fasta`. If `FALSE`, reads are assumed to be single-end and just one file, `fname.fasta`, is written.
`gzip`	If `TRUE`, gzip the output fasta files.
`offset`	An integer number greater or equal to 1 to start assigning read numbers at.

The get_reads function returns a DNAStringSet object representing sequencing reads that can be directly passed to write_reads. If output other than that from get_reads is used and paired is TRUE, make sure reads is ordered properly (i.e., that mate pairs appear together and that the left mate appears first).

No return, but FASTA file(s) containing the sequences in reads are written to fname.fasta (if paired is FALSE) or fname_1.fasta and fname_2.fasta if paired is TRUE.

get_reads

  library(Biostrings)
  data(srPhiX174) # pretend srPhiX174 represents a DNAStringSet of *reads*
  readlen = unique(width(srPhiX174)) #35
  write_reads(srPhiX174, fname='./srPhiX174', readlen=readlen, paired=FALSE,
      gzip=FALSE)

## If the file is too big, you can subset it and write it in chunks.
## Here we split our 'reads' into two chunks and save them to the same file.
write_reads(srPhiX174[1:100], fname='./srPhiX174-offset', readlen=readlen,
   paired=FALSE, gzip=FALSE, offset = 1L)
write_reads(srPhiX174[101:length(srPhiX174)], fname='./srPhiX174-offset',
   readlen=readlen, paired=FALSE, gzip=FALSE, offset = 101L)

## We can verify that we get the same results
srPhi <- readDNAStringSet('./srPhiX174.fasta')
srPhiOffset <- readDNAStringSet('./srPhiX174-offset.fasta')
identical(srPhi, srPhiOffset)