write.listedDNAStringSet: Write a fasta file per sample in parallel

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

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

Usage

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

Arguments

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.

Note

• 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

See Also

findBarcodes, read.SeqFolder, extractSeqs, addListNameToReads

Examples

 
## Not run: 
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)

## End(Not run)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.