phylotools (version 0.2.2)

rm.sequence.fasta: Delete sequences from fasta file

Description

Delete sequences from fasta file

Usage

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.

Value

This is a subroutine without return value.

Details

Delete sequences from a fasta file.

References

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

See Also

read.fasta, dat2fasta

Examples

# NOT RUN {
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"))

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