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RiboCode/RiboTISH helpers

RiboCode/RiboTISH helpers convert external ORF-calling results into formats that can be reused in downstream annotation, visualization, and sequence extraction steps.

RiboCode helper

ribocode_bed_format

Function

Convert RiboCode BED-format ORF output into GenePred format. The command can filter ORFs by class and minimum amino-acid length, then adjusts the terminal stop-codon boundary before writing the GenePred table.

Parameters

Parameter Meaning
-i Input RiboCode BED file.
-o Output prefix. The final file is <prefix>.genepred.
-t ORF class to keep: all, smorf, or annotated. Default: all.
-l Minimum amino-acid length. Default: 8.
-c Declared as “drop fuzzy ORFs”; currently reserved and not applied by the implementation.

ORF class behavior

-t value Kept ORF types
all All ORF types that pass length filtering.
smorf uORF, dORF, novel, dORF,novel, uORF,novel.
annotated internal, annotated.

Example

ribocode_bed_format \
  -i RiboCode_ORFs.bed \
  -t smorf \
  -l 8 \
  -o RiboCode.smorf

Output file:

RiboCode.smorf.genepred

Output GenePred columns

The output is a headerless GenePred-like table:

name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds

Notes

  • ribocode_bed_format derives ORF length from the ORF name suffix. Make sure the RiboCode BED name field follows the expected naming convention.
  • The generated GenePred files are headerless; add headers manually only if a downstream tool expects them.