Installation

To install geneRFinder, please running the script follow:

Rscript ./src/config.R

Usage

To run geneRFinder,

Rscript ./geneRFinder.R -i [fasta_file_name] -o [output_file_name] -t [thread_number] -s [start_type] -n [intergenic]

[fasta_file_name]: input file name

[output_file_name]: output file name

[thread_number]: number of thread

[start_type]:
            1 - if start codon is ATG
            2 - if start codon is ATG, GTG and TTG

[intergenic]:
            1 - output without intergenic sequences
            2 - output with intergenic sequences

For example,

Rscript ./geneRFinder.R -i ./example/final.contigs.fa -o output -t 7 -s 1 -n 1

Please, download the src/model.RData file separately, it is a large file.

Output

In the output there are for each sequence:

>[random_id], [sequence_length],[contig_id]
[sequence]

[random_id]: a random id, for control

[sequence_length]: length of the sequence

[contig_id]: the id from the contig

[sequence]: the gene or intergenic generated

Example:

>34, len=63, k121_33 flag=1 multi=2.0000 len=501
ATGATAAAAGCGCGCGTCAGGTACGGCTCGTCGCCGCCGGCAATGCCTATGCGGTCACGCTAA