read.dna: Read DNA Sequences in a File

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/read.dna.R

Description

These functions read DNA sequences in a file, and returns a matrix or a list of DNA sequences with the names of the taxa read in the file as rownames or names, respectively. By default, the sequences are stored in binary format, otherwise (if as.character = TRUE) in lowercase.

Usage

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read.dna(file, format = "interleaved", skip = 0,
         nlines = 0, comment.char = "#",
         as.character = FALSE, as.matrix = NULL)
read.FASTA(file, type = "DNA")
read.fastq(file, offset = -33)

Arguments

file

a file name specified by either a variable of mode character, or a double-quoted string. Can also be a connection (which will be opened for reading if necessary, and if so closed (and hence destroyed) at the end of the function call).

format

a character string specifying the format of the DNA sequences. Four choices are possible: "interleaved", "sequential", "clustal", or "fasta", or any unambiguous abbreviation of these.

skip

the number of lines of the input file to skip before beginning to read data (ignored for FASTA files; see below).

nlines

the number of lines to be read (by default the file is read untill its end; ignored for FASTA files)).

comment.char

a single character, the remaining of the line after this character is ignored (ignored for FASTA files).

as.character

a logical controlling whether to return the sequences as an object of class "DNAbin" (the default).

as.matrix

(used if format = "fasta") one of the three followings: (i) NULL: returns the sequences in a matrix if they are of the same length, otherwise in a list; (ii) TRUE: returns the sequences in a matrix, or stops with an error if they are of different lengths; (iii) FALSE: always returns the sequences in a list.

type

a character string giving the type of the sequences: one of "DNA" or "AA" (case-independent, can be abbreviated).

offset

the value to be added to the quality scores (the default applies to the Sanger format and should work for most recent FASTQ files).

Details

read.dna follows the interleaved and sequential formats defined in PHYLIP (Felsenstein, 1993) but with the original feature than there is no restriction on the lengths of the taxa names. For these two formats, the first line of the file must contain the dimensions of the data (the numbers of taxa and the numbers of nucleotides); the sequences are considered as aligned and thus must be of the same lengths for all taxa. For the FASTA and FASTQ formats, the conventions defined in the references are followed; the sequences are taken as non-aligned. For all formats, the nucleotides can be arranged in any way with blanks and line-breaks inside (with the restriction that the first ten nucleotides must be contiguous for the interleaved and sequential formats, see below). The names of the sequences are read in the file. Particularities for each format are detailed below.

The FASTQ format is explained in the references.

Compressed files must be read through connections (see examples). read.fastq can read compressed files directly (see examples).

Value

a matrix or a list (if format = "fasta") of DNA sequences stored in binary format, or of mode character (if as.character = "TRUE").

read.FASTA always returns a list of class "DNAbin" or "AAbin".

read.fastq returns a list of class "DNAbin" with an atrribute "QUAL" (see examples).

Author(s)

Emmanuel Paradis and RJ Ewing

References

Anonymous. FASTA format. https://en.wikipedia.org/wiki/FASTA_format

Anonymous. FASTQ format. https://en.wikipedia.org/wiki/FASTQ_format

Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington. http://evolution.genetics.washington.edu/phylip/phylip.html

See Also

read.GenBank, write.dna, DNAbin, dist.dna, woodmouse

Examples

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## a small extract from data(woddmouse) in sequential format:
cat("3 40",
"No305     NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
"No304     ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
"No306     ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
file = "exdna.txt", sep = "\n")
ex.dna <- read.dna("exdna.txt", format = "sequential")
str(ex.dna)
ex.dna
## the same data in interleaved format...
cat("3 40",
"No305     NTTCGAAAAA CACACCCACT",
"No304     ATTCGAAAAA CACACCCACT",
"No306     ATTCGAAAAA CACACCCACT",
"          ACTAAAANTT ATCAGTCACT",
"          ACTAAAAATT ATCAACCACT",
"          ACTAAAAATT ATCAATCACT",
file = "exdna.txt", sep = "\n")
ex.dna2 <- read.dna("exdna.txt")
## ... in clustal format...
cat("CLUSTAL (ape) multiple sequence alignment", "",
"No305     NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
"No304     ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
"No306     ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
"           ************************** ******  ****",
file = "exdna.txt", sep = "\n")
ex.dna3 <- read.dna("exdna.txt", format = "clustal")
## ... and in FASTA format
cat(">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
">No304",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
">No306",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
file = "exdna.fas", sep = "\n")
ex.dna4 <- read.dna("exdna.fas", format = "fasta")
## They are the same:
identical(ex.dna, ex.dna2)
identical(ex.dna, ex.dna3)
identical(ex.dna, ex.dna4)

## How to read compressed files:

## create the ZIP file:
zip("exdna.fas.zip", "exdna.fas")
## create the GZ file with a connection:
con <- gzfile("exdna.fas.gz", "wt")
cat(">No305", "NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
    ">No304", "ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
    ">No306", "ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
    file = con, sep = "\n")
close(con)

ex.dna5 <- read.dna(unz("exdna.fas.zip", "exdna.fas"), "fasta")
ex.dna6 <- read.dna(gzfile("exdna.fas.gz"), "fasta")
identical(ex.dna5, ex.dna4)
identical(ex.dna6, ex.dna4)

unlink("exdna.txt")
unlink("exdna.fas")
unlink("exdna.fas.zip")
unlink("exdna.fas.gz")

## read a FASTQ file from 1000 Genomes:
## Not run: 
a <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/sequence_read/"
b <- "SRR062641.filt.fastq.gz"
URL <- paste0(a, b)
download.file(URL, b)
X <- read.fastq(b)
X # 109,811 sequences
## get the qualities of the first sequence:
(qual1 <- attr(X, "QUAL")[[1]])
## the corresponding probabilities:
10^(-qual1/10)
## get the mean quality for each sequence:
mean.qual <- sapply(attr(X, "Q"), mean)
## can do the same for var, sd, ...

## End(Not run)

ape documentation built on July 1, 2020, 10:33 p.m.