circSeqExt: Generating full length circRNA sequences

In tofazzal4720/FcircSEC: Full Length Circular RNA Sequence Extraction and Classification

Description

This function can extract the full length circRNA sequences from the output of the circular RNA predictions tools

Usage

circSeqExt(genomic_seq, circ_class_txt, out_filename)

Arguments

genomic_seq	A fasta file (obtain using function get.fasta) with the genomic sequences for circRNAs
circ_class_txt	The circRNA classification file (obtained from function circClassification)
out_filename	The name of the output file

Value

The fasta file containing the full length circRNA sequences will be written in the output file 'out_filename'

Examples

#Loading an example circRNA genomic sequence and write to a file
#Here temporary directory is created as input-output
#directory. Please provide you own directory instead.
out_dir<-tempdir()
circ_genomic_seq<-data("circRNA_genomic_sequence")
circ_genomic_seq<-circRNA_genomic_sequence
df.fasta=dataframe2fas(circ_genomic_seq, file.path(out_dir, "circ_genomic_seq.fasta"))

#Loading an example circ_class_txt data and write to a file
circ_class_txt<-data("circRNA_classt")
circ_class_txt<-circRNA_classt
write.table(circ_class_txt, file.path(out_dir, "circ_class.txt"), 
        row.names=FALSE)

#Extracting full length circRNA sequences. Here, the output will be 
#written in file circRNA_sequence.fasta in out_dir directory
circSeqExt(file.path(out_dir, "circ_genomic_seq.fasta"),
 file.path(out_dir, "circ_class.txt"), file.path(out_dir, "circRNA_sequence.fasta"))

tofazzal4720/FcircSEC documentation built on Jan. 26, 2020, 7:50 a.m.