loadFasta | R Documentation |
Read/write a FASTA file from/to disk
loadFasta( file = "file.fasta", verbose = TRUE, short.desc = TRUE)
writeFasta( fasta, file = NULL, line.width = 80)
writeLongFasta( desc, seq, file = NULL)
file |
complete path name to an existing FASTA file for |
short.desc |
logical, should the descriptor text be truncated at the first blank character |
fasta |
a fasta object, with 'desc' and 'seq' named elements |
desc |
character vector of descriptors |
seq |
character vector of sequences |
line.width |
integer value, the maximum line wrap length for written FASTA files |
loadFasta is a wrapper around the Biostrings function 'readBStringSet'.
The 'LongFasta' is a faster version that bypasses the line wrapping step, writing the entire sequence on a single line
For loadFasta
, a list of length 2, with:
desc |
character vector of descriptors, from the '>' lines of the FASTA file |
seq |
character vector of sequences |
as.Fasta
for making fasta objects
getFastaSeqFromFilePath
, for getting the genomic sequence for a specific
chrmosome.
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