usage: annogesic [-h] [--version]
                 {create,get_input_files,get_target_fasta,annotation_transfer,expression_analysis,tsspredator,optimize_tsspredator,color_png,terminator,transcript_assembly,utr,srna,sorf,promoter,operon,circrna,go_term,srna_target,snp,ppi_network,subcellular_localization,riboswitch,screenshot}
                 ...

positional arguments:
  {create,get_input_files,get_target_fasta,annotation_transfer,expression_analysis,tsspredator,optimize_tsspredator,color_png,terminator,transcript_assembly,utr,srna,sorf,promoter,operon,circrna,go_term,srna_target,snp,ppi_network,subcellular_localization,riboswitch,screenshot}
                        commands
    create              Create a project
    get_input_files     Get required files. (i.e. annotation files, fasta
                        files)
    get_target_fasta    Get target fasta.
    annotation_transfer
                        Run RATT to transfer the annotation files from
                        reference to target.
    tsspredator         Run TSSpredator to predict TSSs or processing sites.
    optimize_tsspredator
                        Optimize TSSpredator based on (partial)manual detect
                        one.
    color_png           Generating color screenshots of TSS or processing
                        site. It only works after running batch script.
    terminator          Detect Terminators.
    transcript_assembly
                        Run transcriptome assembly for detecting transcripts.
    utr                 Run UTR detection to detect 5'UTR and 3'UTR.
    srna                Run sRNA detection to detect sRNA candidates.
    sorf                Run sORF detection to detect sORF candidates which has
                        expression.
    promoter            Run MEME to dicover promoter.
    operon              Detect operon and combine features together.
    circrna             Detect circular RNA.
    go_term             Extract and find Go terms.
    srna_target         sRNA target prediction.
    snp                 Detection of SNP of transcripts.
    ppi_network         Generate protein-protein interaction with literature
                        supported.
    subcellular_localization
                        Prediction of subcellular localization of genomic CDS.
    riboswitch          Prediction of riboswitch.
    screenshot          Generate screenshot for selected feature.

optional arguments:
  -h, --help            show this help message and exit
  --version, -v         show version