write2FASTA: Write sequences to a file in fasta format

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Write sequences to a file in fasta format

Description

Write the sequences obtained from getAllPeakSequence to a file in fasta format leveraging writeFASTA in Biostrings package. FASTA is a simple file format for biological sequence data. A FASTA format file contains one or more sequences and there is a header line which begins with a > proceeding each sequence.

Usage

write2FASTA(mySeq, file = "", width = 80)

Arguments

mySeq	GRanges with varibles name and sequence ,e.g., results obtained from getAllPeakSequence
file	Either a character string naming a file or a connection open for reading or writing. If "" (the default for write2FASTA), then the function writes to the standard output connection (the console) unless redirected by sink
width	The maximum number of letters per line of sequence

Value

Output as FASTA file format to the naming file or the console.

Author(s)

Lihua Julie Zhu

Examples

peaksWithSequences = GRanges(seqnames=c("1", "2"),
IRanges(start=c(1000, 2000), 
end=c(1010, 2010), 
names=c("id1", "id2")), 
sequence= c("CCCCCCCCGGGGG", "TTTTTTTAAAAAA"))

write2FASTA(peaksWithSequences, file="testseq.fasta", width=50)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.