Description Usage Arguments Value Examples
View source: R/get_fasta_utils.R
Generate n-random sequences of pre-determined length from given input multi-fasta file
1 2 3 4 5 6 7 8 | get_random_sequences_from_fasta(
fasta_file,
numberOfRandomSequences = 50,
lengthOfRandomSequence = 100,
write_bed = FALSE,
write_outputfasta = FALSE,
outfile = "randomSeq"
)
|
fasta_file |
Either a path or a connection to reference multi-fasta file, from which subset of sequences for given input feature is to be retrieved. In the sequence header: only string before first space and/or first colon (:) will be considered for further processes. **Important consideration when header have long names. |
numberOfRandomSequences |
Numeric, number of random sequences to be generated. |
lengthOfRandomSequence |
Numeric, length of random sequences. |
write_bed |
Logical, to return flank region as a output bed file, Default: FALSE |
write_outputfasta |
Logical, to return flank sequences as a output multi-fasta file, Default: FALSE |
outfile |
character vector, defining output file name, Default: 'flank_out' |
A ranges of random regions and respective random sequences.
1 2 3 4 5 6 7 8 9 10 | ## Not run:
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")
fastaR::get_random_sequences_from_fasta(fasta_file = ref_fasta,
numberOfRandomSequences = 100,
lengthOfRandomSequence = 500)
## End(Not run)
|
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