raise ValueError("can only convert an array of size 1 to a Python scalar")

[gnilihzeux]

Dear author,
There is an error in my running, how should i solved it?

ValueError: can only convert an array of size 1 to a Python scalar
running: ['miniconda3/envs/rMATS-long/bin/python', 'miniconda3/envs/rMATS-long/rMATS-long/FindAltTSEvents.py'
, '-i', 'li.et.al.2023_human_vascular_smooth_muscle_cells/04-alternative_splicing/ENSG00000174748.22_isoform_diffe
rences_ENST00000307839.10_to_ENST00000307839.10-03d8ejcvf_tmp_isoform.gtf', '-o', 'li.et.al.2023_human_vascular_sm
ooth_muscle_cells//04-alternative_splicing/ENSG00000174748.22_isoform_differences_ENST00000307839.10_to_ENST00000307839.10-0.tsv']
Traceback (most recent call last):
  File "miniconda3/envs/rMATS-long/rMATS-long/classify_isoform_differences.py", line 179, in <module>
    main()
  File "miniconda3/envs/rMATS-long/rMATS-long/classify_isoform_differences.py", line 175, in main
    classify_isoform_differences(args)
  File "miniconda3/envs/rMATS-long/rMATS-long/classify_isoform_differences.py", line 55, in classify_isoform_differences
    classify_isoform_differences_with_temp_files(
  File "miniconda3/envs/rMATS-long/rMATS-long/classify_isoform_differences.py", line 152, in classify_isoform_differences_with_temp_files
    rmats_long_utils.run_command(command)
  File "miniconda3/envs/rMATS-long/rMATS-long/rmats_long_utils.py", line 283, in run_command
    subprocess.run(command, check=True)
  File "miniconda3/envs/rMATS-long/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
    ```

[EricKutschera]

It looks like ValueError: can only convert an array of size 1 to a Python scalar could be from .item() on a pandas object: https://stackoverflow.com/questions/61705173/pandas-can-only-convert-an-array-of-size-1-to-a-python-scalar

I think the error is from

rMATS-long/scripts/FindAltTSEvents.py

Line 225 in 6961a37

strand = transcriptDF[transcriptDF[8].str.contains(transcript)][6].item()

The -o argument to the script was li.et.al.2023_human_vascular_smooth_muscle_cells//04-alternative_splicing/ENSG00000174748.22_isoform_differences_ENST00000307839.10_to_ENST00000307839.10-0.tsv which includes the two transcripts to compare: ENST00000307839.10 and ENST00000307839.10-0.

The script looks up info in the .gtf file by finding the line that contains the transcript ID. In this case ENST00000307839.10 is a substring of ENST00000307839.10-0 and it finds two lines that match the shorter ID

What was the original command you ran and did the original input files contain ENST00000307839.10-0?

[gnilihzeux]

Thank you for your reply.

Actually, the problem has already arisen at visualize_isoforms.py. ENST00000307839.10-0 is a isoform of ENST00000307839.10 from flair.

rMATS-long is installed from conda. My command

python ${RMATS}/rmats_long.py --abundance abundace.esp --updated-gtf updated_gtf --gencode-gtf gencode.gtf --group-1 group_1.txt --group-2 group_2.txt --group-1-name $GRP1 --group-2-name $GRP2 --out-dir $AS_DIR --num-threads 16 --use-unadjusted-pvalue

The files about ENSG00000174748.22 are uploaded for your review.
(.gtf and .esp has been added a .txt extention for upload)

ENSG00000174748.22.abundance.esp.txt
gencode.gtf.txt
group_1.txt
group_2.txt
updated.gtf.txt

[EricKutschera]

I think this code should handle one transcript ID being a substring of another: #16