ncORF classification

orf_type.py

Classification of non-canonical ORFs based on Mudge JM et al. 2022. Preferred input is genomic coordinates of ncORFs in bed12 format (columns 5,7-9 are useless and simple placerholders are allowed). Outputs of predicted translated ORFs by PRICE, RiboCode, Ribo-TISH, and RibORF are also supported. TXINFO file can be generated by gtf.py txinfo from GPP with parameter -f.

usage: python orf_type.py -h

Usage: orf_type.py [OPTIONS] PATH_ORF_PRED PATH_GTF PATH_TXINFO

  A pipeline for the classification of non-canonical ORFs

  path_orf_pred: path to predicted ORFs
  path_gtf: path to gtf file
  path_txinfo: path to transcript info file (e.g., generated by extract_txinfo_ensembl.R)

Options:
  -m, --pred_method [price|ribocode|riborf|ribotish|bed12|tabular]
                                  ORF prediction method  [default: price]
  -p, --prefix TEXT               output prefix  [default: orfpred]
  -k, --keep_cds                  whether to keep annotated CDSs and their
                                  variants
  -h, --help                      Show this message and exit.