usage: cORF_predictio_pipeline.py [input data]
input data:
-circ , -ci, -c
A file with the circles locations in the format as in example file : circ_example_dm3.txt
-annotation, -a, -A Annotation file in the format as in example file : annotation_example_dm3.txt
-system,-sys,-Sys full path to fasta file of the genome
-output, -o, -O output file name.
optional:
--force_exact Use only circRNA with junction on annotaed exons boundaries
--collapse_frames report only one cORF for each circRNA. Choose the longest ORF.