Error when writing transcripts to file

[ewallace]

Hi, RiboCode runs on my dataset from Cryptococcus neoformas, then fails during the writing to gtf. This meant that ORF calling succeeded and wrote a complete .txt file, but for the .gtf output left large gaps of entire chromosomes or half-chromosomes.

Error message was: Errors: 88% has finished! Writing the results to file ..... error when transform the transcript interval to genomic! Traceback (most recent call last): File "/usr/local/bin/RiboCode", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python3.6/dist-packages/RiboCode/RiboCode.py", line 63, in main output_gtf=output_gtf, output_bed=output_bed) File "/usr/local/lib/python3.6/dist-packages/RiboCode/detectORF.py", line 455, in main write_to_gtf(gene_dict, transcript_dict, orf_results, collapsed_orf_idx, outname) File "/usr/local/lib/python3.6/dist-packages/RiboCode/detectORF.py", line 192, in write_to_gtf exon_ivs = transcript_iv_transform(tobj, orf_iv) File "/usr/local/lib/python3.6/dist-packages/RiboCode/prepare_transcripts.py", line 285, in transcript_iv_transform exons_ivs.append(Interval_from_directional(exons_bound[i],exons_bound[i+1],strand))

I suggest three possible ways to help with this.

1. Report which transcript / exon has failed.
2. Put some exception-handling code around that failure so that remaining transcripts are still written.
3. Write out the ORFs in transcript co-ordinates first, which would be better for my application anyway.

I can provide access to data and annotations if that helps to debug!

Thanks Edward