[BUG] FEELnc_tpLevel2gnLevelClassification.R

[silvaib]

Hello!

When installing FEELnc via conda, the script FEELnc_tpLevel2gnLevelClassification.R fails with a syntax error:

miniconda3/envs/feelnc/bin/FEELnc_tpLevel2gnLevelClassification.R: 9: Syntax error: "(" unexpected

Cloning the repository directly avoids this syntax error, but I still cannot run the script successfully with either the provided test data or my own data due to a different error.

With the test data, I get:

- annotation gene : (1)
100 / 254
200 / 254
- annotation gene (2):
Error in strsplit(annotation_gene$feelLncPcgClassNameByTp[i], ";") :
  non-character argument
Calls: data.frame -> unlist -> strsplit
Execution halted

Command used:

Rscript scripts/FEELnc_tpLevel2gnLevelClassification.R \
  test/annotation_chr38.gtf \
  test/results/classifier/candidate_lncRNA_classes.txt \
  test/results/classifier/candidate_lncRNA.gtf.lncRNA.feelncclassifier.log

With other GTF files available in the test data, just in case I used the wrong one, I get:

Error in data.frame(gnId = gtf_transcripts$gene_id, gnName = gtf_transcripts$gene_name,  :
  arguments imply differing number of rows: 0, 1
Execution halted

Environment:

• Conda version: 25.1.1
• R version: 4.1.3
• FEELnc version: conda = 0.2 ; git clone = 0.2.1

Installation method: conda install -c bioconda feelnc

Thank you for FEELnc! Let me know if you need any additional logs or environment details.