rm.sequence.fasta: Delete sequences from fasta file

In phylotools: Phylogenetic Tools for Eco-Phylogenetics

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.

Details

Delete sequences from a fasta file.

Value

This is a subroutine without return value.

Author(s)

Jinlong Zhang <[e-mail]>

References

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

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"))

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

phylotools documentation built on May 2, 2019, 3:25 a.m.