xpore v2.0 dataprep ERROR

Hi developer, I’m trying to using the practice demo data downloaded from https://zenodo.org/record/5103099/files/demo.tar.gz, and I have successfully installed the latest version of xpore version 2.0. When I came to the step of dataprep, I kept getting the same ERROR and could not proceed, it seemed that something wrong happened to the index.

My working directory: ~/bioinfo/xpore_practice/demo/data/HEK293T-WT-rep1

The running command:

xpore dataprep \
--eventalign nanopolish/eventalign.txt \
--gtf_path_or_url demo.gtf \
--transcript_fasta_paths_or_urls demo.fa \
--out_dir dataprep \
--genome

And then came this ERROR: /home/huangkx/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py:3607: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self._set_item(key, value) /home/huangkx/miniconda3/lib/python3.9/site-packages/xpore/scripts/dataprep.py:21: PerformanceWarning: indexing past lexsort depth may impact performance. pos_end += eventalign_result.loc[index][‘line_length’].sum() Traceback (most recent call last): File “/home/huangkx/miniconda3/bin/xpore”, line 33, in <module> sys.exit(load_entry_point(‘xpore==2.0’, ‘console_scripts’, ‘xpore’)()) File “/home/huangkx/miniconda3/lib/python3.9/site-packages/xpore/scripts/xpore.py”, line 67, in main options.func(options) File “/home/huangkx/miniconda3/lib/python3.9/site-packages/xpore/scripts/dataprep.py”, line 688, in dataprep merge_transcript_id_version = check_gene_tx_id_version(gtf_path_or_url) File “/home/huangkx/miniconda3/lib/python3.9/site-packages/xpore/scripts/dataprep.py”, line 635, in check_gene_tx_id_version if ln[2] == “transcript” or ln[2] == “exon”: IndexError: list index out of range

It would be grateful if you could give me some advice on solving this problem. Thanks for developing this nice tool.

[ploy-np]

Hi @DrDaedalusWHU,

I have updated the demo.tar.gz file already. Could you please try again? Note that the download link is changed to https://zenodo.org/record/5162402/files/demo.tar.gz

[DrDaedalusWHU]

Thanks for your kind reply! I will try the newly uploaded demo files.