import.fasta {Bios2cor} | R Documentation |
Reads a file in FASTA format
Description
Reads a Multiple Sequence Alignment (MSA) file in FASTA format (.fasta or .fa extension).
Usage
import.fasta(file, aa.to.upper = TRUE, gap.to.dash = TRUE, log.file = NULL)
Arguments
file |
a string of characters to indicate the name of the MSA file to be read. |
aa.to.upper |
a logical value indicating whether amino acids should be converted to upper case (TRUE) or not (FALSE). Default is TRUE. |
gap.to.dash |
a logical value indicating whether the dot (.) and tilde ( |
log.file |
a file containing errors that occurred when trying to read fasta file |
Details
Initially, FASTA (for FAST-ALL) was the input format of the FASTA program, used for protein comparison and searching in databases. Presently, FASTA format is a standard format for biological sequences.
The FASTA formatted file of a single sequence displays:
a single-line description beginning with a greater-than (>) symbol. The following word is the identifier.
followed by any number of lines, representing biological sequence.
For multiple alignments, the FASTA formatted sequences are concatenated to create a multiple FASTA format.
Value
A object of class 'align', which is a named list whose elements correspond to sequences, in the form of character vectors.
Note
The import.fasta
function was developed for the bios2mds
R package (Julien PELE [aut], Jean-Michel BECU [aut], Marie CHABBERT [cre]).
.
Author(s)
Julien PELE
References
Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 27:2444-2448.
Examples
# Importing MSA file in FASTA format
aln <- import.fasta(system.file("msa/toy2_align.fa", package = "Bios2cor"))