readFastaFile {krm}

Read a Fasta Sequence File

Description

Read a Fasta Sequence File

Usage

readFastaFile(fileName, sep = " ")
writeFastaFile (seqList, fileName)
aa2arabic (seq1) 
string2arabic (seqList) 
fastaFile2arabicFile (fastaFile, arabicFile, removeGapMajor=FALSE)
selexFile2arabicFile (selexFile, arabicFile, removeGapMajor=FALSE)
stringList2arabicFile (seqList, arabicFile, removeGapMajor=FALSE)
arabic2arabicFile (alignment, arabicFile) 
readSelexFile (fileName)
readSelexAsMatrix (fileName) 
arabic2fastaFile (alignment, fileName)
readArabicFile (fileName) 
readBlockFile (fileName) 

Arguments

fileName

string

fastaFile

string

arabicFile

string

selexFile

string

sep

string

seq1

string. A string of amino acids

seqList

list of string.

removeGapMajor

Boolean

alignment

matrix of arabic representation of sequences (1 based)

Value

string2arabic returns a matrix of arabic numbers representing aa. readSelexFile return a list of strings. readArabicFile return a matrix of n by p alignment.

Examples

library(RUnit)
fileName=paste(system.file(package="krm")[1],'/misc/SETpfamseed_aligned_for_testing.fasta', sep="")
seqs = readFastaFile (fileName, sep=" ")
checkEquals(length(seqs),11)