[Bug]: IndexError: list index out of range

[shin0727]

Describe the bug

I got error in
"flair/lib/python3.10/site-packages/flair/gtf_to_bed.py", line 108, in
if blockcount > 1 and blockstarts[0] > blockstarts[1]: # need to reverse exons"

IndexError: list index out of range

To Reproduce

flair collapse -g ${REF} --gtf ${EGAPX_GTF} -q ../../02_correct/${PREFIX}/${PREFIX}_all_corrected.bed -r ${FASTQ} --stringent --check_splice --generate_map --annotation_reliant generate --output ${PREFIX} --thread ${THREAD}

Expected behavior

${PREFIX}_scaf.annotated_transcripts.bed

Logs and Stack traces

Traceback (most recent call last):
  File "/home/junkim/tools/miniconda3/envs/flair/lib/python3.10/site-packages/flair/gtf_to_bed.py", line 108, in <module>
    if blockcount > 1 and blockstarts[0] > blockstarts[1]:  # need to reverse exons
IndexError: list index out of range

Screenshots

Additional Context

ModuleNotFoundError: No module named 'torch'

Environment

ModuleNotFoundError: No module named 'torch'

[helpmefindaname]

Hi @shin0727
it looks to me, like you are trying to use a different library that has the same name as ours.
I can ensure you that in our library:

• flair collapse isn't a valid command, as we are not providing any installable scripts.
• flair/gtf_to_bed.py doesn't exist.
• torch would be installed as a dependency when installing flair.

If you intend to use flair-brookslab then you might be better off to contact the authors of that library.