IndexError: list index out of range tama_filter_primary_transcripts_orf.py

[bijendrabio]

Hello, I received following error while running tama_filter_primary_transcripts_orf.py on tama collapsed bed file. Kindly suggest!. self.prot_id = id_split[2] IndexError: list index out of range

[GenomeRIK]

Hello,

Thank you for using TAMA.

Can you show me the exact command line that you used to run the script? I suspect you are using the incorrect input files.

Thank you, Richard

[bijendrabio]

Hello Richard, Here's a command and error output: COMMAND LINE: tama_filter_primary_transcripts_orf.py -b tama_collapse_output.bed -o tama_collapse_output_filter

ERROR: opening bed file Traceback (most recent call last): File "/home/envs/tama/bin/tama_filter_primary_transcripts_orf.py", line 229, in trans_obj.id_parser(id_line) File "/home/envs/tama/bin/tama_filter_primary_transcripts_orf.py", line 137, in id_parser self.prot_id = id_split[2] IndexError: list index out of range

[GenomeRIK]

Hello,

That tool is for use with a bed file that is produced using the TAMA ORF/NMD pipeline only. It looks like you are trying to use the bed file from the TAMA collapse run which will not work since it does not contain all the information needed.

Could you explain what you are wanting to get?

Thank you, Richard

[bijendrabio]

Hello, I am trying to remove overlapping transcripts (isoforms), keeping only the longest ORF containing transcript per gene loci. is there a way to do this using the available tama supporting scripts?

See https://github.com/GenomeRIK/tama/issues/29 for context

Regards, B

[GenomeRIK]

Hello B,

You will need to run the TAMA ORF/NMD prediction pipeline as seen here: https://github.com/GenomeRIK/tama/wiki/TAMA-GO:-ORF-and-NMD-predictions

And then use the output from that pipeline to run "tama_filter_primary_transcripts_orf.py".

Cheers, Richard