An error occurred while running 'get_longest_isoform.py'

MICHELLE-LMX commented 1 year ago

Hi, I ran 'get_longest_isoform.py' using the files under the TSEBRA/example/tsebra_workdir/ path and the following error occurred.

I used the following command: /TSEBRA/bin/get_longest_isoform.py -g braker1.gtf,braker2.gtf -o combined12.gtf

I got the following error:

READING GENE PREDICTION: [braker1.gtf]

READING GENE PREDICTION: [braker2.gtf]

BUILD OVERLAP GRAPH

CHOOSE LONGEST ISOFORM FOR EACH GENE

Traceback (most recent call last): File "/TSEBRA/bin/get_longest_isoform.py", line 107, in main() File "/TSEBRA/bin/get_longest_isoform.py", line 63, in main tx_longest = sorted([graph.tx_from_key(n) for \ File "/TSEBRA/bin/get_longest_isoform.py", line 64, in n in comp], key=lambda t:t.get_cds_len())[-1] AttributeError: 'Transcript' object has no attribute 'get_cds_len'

Any suggestion on a solution? Thanks, Michelle

jmpolinski commented 1 year ago

Any update on the cause/solution for this error message? I just got the same one

LarsGab commented 1 year ago

Hi,

this has been fixed in commit b134a523481904c600a3b4f894cab7db937d5cb2 . Best, Lars

sahoo-rk commented 9 months ago

I execute the script with a single braker.gtf file and the error still persists in the updated version.

get_longest_isoform.py --gtf braker.gtf --out longiso.gtf

### READING GENE PREDICTION: [braker.gtf]
### BUILD OVERLAP GRAPH
### CHOOSE LONGEST ISOFORM FOR EACH GENE
Traceback (most recent call last):
  File "/home/sahoork/dumpack/TSEBRA/bin/get_longest_isoform.py", line 107, in <module>
    main()
  File "/home/sahoork/dumpack/TSEBRA/bin/get_longest_isoform.py", line 63, in main
    tx_longest = sorted([graph.__tx_from_key__(n) for \
  File "/home/sahoork/dumpack/TSEBRA/bin/get_longest_isoform.py", line 64, in <lambda>
    n in comp], key=lambda t:t.get_cds_len())[-1]
AttributeError: 'Transcript' object has no attribute 'get_cds_len'

Am I missing something? Please suggest.

Thanks,

Gaius-Augustus / TSEBRA