get.fasta: Generating sequences from the reference genome with specific...

In FcircSEC: Full Length Circular RNA Sequence Extraction and Classification

Description

This function can extract the sequences from the reference genome for the given intervals (start, end) of chromosomes

Usage

get.fasta(ref_genome, circ_class_bed, out_filename)

Arguments

ref_genome	The reference genome
circ_class_bed	The bed file having chromosome, start and end position of each circRNAs (obtained from function circClassification)
out_filename	The name of the output file

Value

The fasta file of the sequences extracted from the reference genome for the given intervals will be written in the output file 'out_filename'

Examples

#Loading an example reference genome and write to a file
#Here temporary directory is created as input-output
#directory. Please provide you own directory instead.
out_dir<-tempdir()
ref_genom<-data("chr1")
ref_genom<-chr1
df.fasta=dataframe2fas(ref_genom, file.path(out_dir, "ref_genome.fasta"))

#Loading an example circRNA classification bed file and write to a file
circ_class_bed<-data("circRNA_classb")
circ_class_bed<-circRNA_classb
write.table(circ_class_bed, file.path(out_dir, "circ_class.bed"), 
    col.names=FALSE, row.names=FALSE)

#Getting genomic sequences of circRNAs. The output will be 
#generated in file circRNA_genomic_seq.fasta in out_dir directory
get.fasta(file.path(out_dir, "ref_genome.fasta"), 
   file.path(out_dir, "circ_class.bed"), 
   file.path(out_dir, "circRNA_genomic_seq.fasta"))

FcircSEC documentation built on Jan. 31, 2020, 5:07 p.m.