readFastaFile | R Documentation |
Read a Fasta Sequence File
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)
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) |
string2arabic returns a matrix of arabic numbers representing aa. readSelexFile return a list of strings. readArabicFile return a matrix of n by p alignment.
library(RUnit) fileName=paste(system.file(package="krm")[1],'/misc/SETpfamseed_aligned_for_testing.fasta', sep="") seqs = readFastaFile (fileName, sep=" ") checkEquals(length(seqs),11)
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