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

Extracting the full length circRNA sequence for the example data provided in FicrcSEC package

Author Md. Tofazzal Hossain, Date: 14.01.2020

Extracting transcript information from the annotation file

library("FcircSEC")

    #Loading an example annotation file and write to a file
    #Here temporary directory is created as input-output
    #directory. Please provide your own directory instead.
    out_dir<-tempdir()
    annotation_file<-data(refGenchr1)  
    annotation_file<-refGenchr1
    write.table(annotation_file, file.path(out_dir,"annotation_file.gtf"), 
         row.names=FALSE, sep="\t",quote=FALSE, col.names=FALSE)

    #Extraction of transcript information. Here, the output will be generated in file 
    #transcriptdata.txt in out_dir directory
    transcriptExtract(file.path(out_dir,"annotation_file.gtf"), "ucsc", 
    file.path(out_dir, "transcriptdata.txt"))

    transdata<-read.table(file.path(out_dir, "transcriptdata.txt"), header = T) # open the output file
    head(transdata) # see the 1st 6 rows

Classifying circRNAs

    #Loading and example transcript data and write to a file
    #Here temporary directory is created as input-output
    #directory. Please provide you own directory instead.
    out_dir<-tempdir()
    t_data<-data("transcript_data") 
    t_data<-transcript_data
    write.table(t_data, file.path(out_dir,"transcript_data.txt"), row.names=FALSE)

    #Loading an example bedfile obtained form the circRNA prediction tool and write to a file
    b_file<-data("output_CIRI")
    b_file<-output_CIRI
    head(b_file) # see the 1st 6 rows
    write.table(b_file, file.path(out_dir,"output_CIRI.bed"), col.names=FALSE, row.names=FALSE)

    #Classification of circRNAs. Here, the output will be written in two files 
    #circRNA_class.txt and circRNA_class.bed in out_dir directory
    circClassification (file.path(out_dir,"transcript_data.txt"), 
            file.path(out_dir,"output_CIRI.bed"), file.path(out_dir, "circRNA_class.txt"), 
              file.path(out_dir, "circRNA_class.bed"))
    #open the output files and see the 1st 6 rows
    circRNA_classt<-read.table(file.path(out_dir, "circRNA_class.txt"), header=T)
    head(circRNA_classt)
    circRNA_classb<-read.table(file.path(out_dir, "circRNA_class.bed"))
    head(circRNA_classb)

Generating sequences from the reference genome with specific intervals

    #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"))
    #open the output file and see the 1st 6 rows
    fastaFile <- readDNAStringSet(file.path(out_dir, "circRNA_genomic_seq.fasta")) 
    seq_name = sub('\\ .*', '', names(fastaFile))
    sequence = paste(fastaFile)
    df <- data.frame(seq_name, sequence)
    head(df)

Generating full length circRNA sequences

    #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"))
    #open the output file and see the 1st 6 rows
    fastaFile1 <- readDNAStringSet(file.path(out_dir, "circRNA_sequence.fasta")) 
    seq_name1 = sub('\\ .*', '', names(fastaFile1))
    sequence1 = paste(fastaFile1)
    df1 <- data.frame(seq_name1, sequence1)
    head(df1)

The End

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