write.listedDNAStringSet: Write a fasta file per sample in parallel
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Note See Also Examples

Given a listed DNAStringSet object return from extractSeqs, the function writes a fasta file for each sample as defined in filePath parameter.

1
2
3

write.listedDNAStringSet(dnaSet, filePath = ".",
  filePrefix = "processed", prependSamplenames = TRUE,
  format = "fasta", parallel = FALSE)

`dnaSet`	listed DNAStringSet object containing sequences to be written.
`filePath`	a path write the fasta files per sample. Default is current working directory.
`filePrefix`	prefix the filenames with a string. Default is 'processed' followed by samplename.
`prependSamplenames`	Prepend definition lines with samplenames. Default is TRUE. Make sure the dnaSet parameter is a named list where names are used as samplenames.
`format`	either fasta (the default) or fastq.
`parallel`	use parallel backend to perform calculation with `BiocParallel`. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using `SerialParam`.

Writing of the files is done using writeXStringSet with parameter append=TRUE. This is to aggregate reads from a sample which might be present in more than one sector.
If data is paired end, then each pair will be written separately with designations in the filename as well as in the definition line as (at)pairX(at) appended at the end.
If parallel=TRUE, then be sure to have a parallel backend registered before running the function. One can use any of the following MulticoreParam SnowParam

findBarcodes, read.SeqFolder, extractSeqs, addListNameToReads

 

load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
samples <- c('Roth-MLV3p-CD4TMLVWell6-Tsp509I', 
'Roth-MLV3p-CD4TMLVWell6-MseI', 'Roth-MLV3p-CD4TMLVwell5-MuA')
seqs <- extractSeqs(seqProps, sector='2', samplename=samples, feature="primed")
write.listedDNAStringSet(seqs)