rename.fasta: Rename the sequences for a fasta file

In helixcn/phylotools: Phylogenetic Tools for Eco-Phylogenetics

Rename the sequences for a fasta file

Description

Rename the sequences within a fasta file according to a data frame supplied.

Usage

rename.fasta(infile = NULL, ref_table, outfile = "renamed.fasta")

Arguments

infile	character string containing the name of the fasta file.
ref_table	a data frame with first column for original name, second column for the new name of the sequence.
outfile	The name of the fasta file with sequences renamed.

Details

If the orginal name was not found in the ref_table, the name for the sequence will be changed into "old_name_" + orginal name.

Value

This is a subroutine without return value.

Note

Since whitespace and punctuation characters will be replaced with "_", name of a sequence might change. It is suggest to obtain the name of the sequences by calling read.fasta first, and save the data.frame to a csv file to obtain the "original" name for the sequences.

Author(s)

Jinlong Zhang <[e-mail]>

References

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

See Also

read.fasta, split_dat

Examples

cat(
    ">seq_1",  "--TTACAAATTGACTTATTATA",
    ">seq_2",  "GATTACAAATTGACTTATTATA",
    ">seq_3",  "GATTACAAATTGACTTATTATA",
    ">seq_5",  "GATTACAAATTGACTTATTATA",
    ">seq_8",  "GATTACAAATTGACTTATTATA",
    ">seq_10", "---TACAAATTGAATTATTATA",
    file = "matk.fasta", sep = "\n")
old_name <- get.fasta.name("matk.fasta")
new_name <- c("Magnolia", "Ranunculus", "Carex", "Morus", "Ulmus", "Salix")
ref2 <- data.frame(old_name, new_name)
rename.fasta(infile = "matk.fasta", ref_table = ref2, outfile = "renamed.fasta")
unlink("matk.fasta")
unlink("renamed.fasta")

helixcn/phylotools documentation built on Oct. 11, 2024, 4:11 a.m.