Delete sequences from fasta file

Delete sequences from fasta file

rm.sequence.fasta(infile, outfile = "sequence.removed.fasta", to.rm = NULL)

Arguments

infile	Character string representing the name of the fasta file.
outfile	Character string representing the name of the output fasta file.
to.rm	Vector of character string containing the names of sequences to be deleted.

Details

Delete sequences from a fasta file.

Value

This is a subroutine without return value.

References

http://www.genomatix.de/online_help/help/sequence_formats.html

Author

Jinlong Zhang <jinlongzhang01@gmail.com>

See also

read.fasta, dat2fasta

Examples

cat(
">seq_1",  "---TCCGCCCCCCTACTCTA",
">seq_3",  "CTCTCCGCCCCTCTACTCTA",
">seq_5",  "---TCCGCCC-TTTACTCTA",
">seq_6",  "---TCCGCCCCTCTACTCTA",
">seq_9",  "---TCCGCCC-TCTACTCTA",
">seq_12", "CTCTCCGCCC-TCTACTCTA",
file = "trn2.fasta", sep = "\n")

rm.sequence.fasta(infile = "trn2.fasta", to.rm = c("seq_1","seq_12"))
#> sequence.removed.fasta has been saved to  /Users/jinlong/Documents/github/phylotools/docs/reference 

unlink("trn2.fasta")
unlink("sequence.removed.fasta")