rename.fasta {phylotools} | R Documentation |
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 <jinlongzhang01@gmail.com>
References
http://www.genomatix.de/online_help/help/sequence_formats.html
See Also
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")