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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.

RiboTISH helper

ribotish_format

Function

Filter RiboTISH ORF prediction output by RiboPvalue, amino-acid length, and ORF class, remove duplicate ORF blocks, and write three downstream files:

Output Description
<prefix>.aa Amino-acid sequences in FASTA format.
<prefix>.cds CDS/nucleotide sequences in FASTA format.
<prefix>.genepred ORF coordinates in GenePred-like format.

Parameters

Parameter Meaning
-i Input RiboTISH result table.
-o Output prefix.
-t ORF class to keep: all, smorf, or annotated. Default: all.
-p Maximum RiboPvalue. Default: 0.05.
-l Minimum amino-acid length, based on AALen. Default: 8.
-c Clean fuzzy/overlapping classes by removing records whose TisType contains Known or CDSFrameOverlap.

ORF class behavior

Before filtering, TisType strings are normalized by replacing 5'UTR with uORF and 3'UTR with dORF.

-t value Kept records
all All records passing p-value and length filtering.
smorf Records whose TisType contains uORF, dORF, or Novel.
annotated Records whose TisType contains Annotated, Extended, Internal, or Truncated.

Required input columns

The input table should contain the RiboTISH output columns used by the formatter, including:

RiboPvalue    AALen    TisType    Gid    Tid    GenomePos    Blocks    AASeq    Seq

Example

ribotish_format \
  -i RiboTISH.results.txt \
  -p 0.05 \
  -l 8 \
  -t smorf \
  -c \
  -o RiboTISH.smorf

Output files:

RiboTISH.smorf.aa
RiboTISH.smorf.cds
RiboTISH.smorf.genepred

Notes

  • ribotish_format removes duplicate ORFs based on TisType and Blocks, keeping the longest ORF after sorting by genomic position and amino-acid length.

  • The generated GenePred files are headerless; add headers manually only if a downstream tool expects them.