sidier (version 1.0)

GetHaplo: Get sequences of unique haplotypes

Description

This function returns the subset of unique sequences composing a given alignment.

Usage

GetHaplo(readfile = T, input = NA, align = NA, saveFile = T, outname = "Haplotypes.txt", format = "fasta", seqsNames = NA)

Arguments

readfile

a logical; if TRUE (default) input alignment is provided as a fasta format in a text file. If FALSE, the alignment is provided as an R object.

input

the name of the fasta file to be analysed.

align

the name of the alignment to be analysed (if "readfile" is set to FALSE,). See "read.dna" in ape package for details about reading alignments.

saveFile

a logical; if TRUE (default), function output is saved as a text file.

outname

if "SaveFile" is set to TRUE (default), contains the name of the output file ("Haplotypes.txt" by default).

format

format of the DNA sequences to be saved: "interleaved", "sequential", or "fasta" (default). See "write.dna" in ape package for details.

seqsNames

names for each DNA sequence saved: Three choices are possible: if n unique sequences are found, "Inf.Hap" assign names from H1 to Hn (according to input order). The second option is to define a vector containing n names. By default, input sequence names

Value

• A file containing unique sequences from the input file.

Details

If two equal sequences are not identically aligned, they will be considered as different haplotypes. To avoid misleading results in uncertain alignments it is recommended to use as input the original unaligned sequences, including gaps after the last nucleotide of short sequences to make all sequence lengths equal.

Examples

cat(">Population1_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence2",
"TTATAGCTGTCGGGCTA------GTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence3",
"GGGGAGCTGTCGGGCTAGTAGCTGTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence4",
"TTATAGCTGTCGGGCTA------GTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population2_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population2_sequence2",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGA----------GTAGAGTATG",
">Population2_sequence3",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAAAAAA",
">Population2_sequence4",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence2",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence3",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence4",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
     file = "ex2.fas", sep = "")
     example2 <- read.dna("ex2.fas", format = "fasta")
	 alin<-read.dna(file="ex2.fas",format="fasta")

 # Reading the alignment from an object and saving haplotypes names as sequential numbers:
GetHaplo(readfile=FALSE,align=alin,outname="Haplotypes_sequentialNames.txt",seqsNames="Inf.Hap")

# Reading the alignment directly from file and saving using sequence input names:
GetHaplo(input="ex2.fas")