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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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Dataprep error #140

Closed rania-o closed 2 years ago

rania-o commented 2 years ago

Hi,

I'm trying to use Xpore to detect modifications on one transcript (440 bp). but I got this error while running the command dataprep :

xpore dataprep --eventalign nanopolish/psi0_transcrit_oligo.eventalign.txt --out_dir dataprep_results --transcript_fasta ../transcript_oligo.fasta

""" 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 chunk_split['line_length'] = np.array(lines) """

-Here is the head of my eventalign.txt file : contig position reference_kmer read_index strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level dystro-oligo 0 GCCAA 0 t 4 78.27 1.380 0.01328GCCAA 73.26 2.11 1.75 dystro-oligo 1 CCAA 0 t 5 92.55 2.484 0.00465CCAA 87.19 3.02 1.31 dystro-oligo 1 CCAA 0 t 6 95.85 1.139 0.00465CCAA 87.19 3.02 2.12 dystro-oligo 2 CAA 0 t 7 98.24 2.083 0.00564CAA 105.72 2.68 -2.06 dystro-oligo 2 CAA 0 t 8 96.94 3.260 0.00598CAA 105.72 2.68 -2.42 dystro-oligo 3 AA 0 t 9 122.06 1.616 0.00299AA 108.90 2.68 3.63 dystro-oligo 4 A 0 t 10 119.61 3.024 0.01295A108.90 2.68 2.95 dystro-oligo 4 A 0 t 11 101.06 3.389 0.00996A108.90 2.68 -2.16

I don't have a GTF file for this sample since it's synthesized, the GTF file is optional right ?

Thank you, Rania

yuukiiwa commented 2 years ago

Hi Rania,

The following several lines are not an error (you can check your dataprep folder whether the outputs are empty):

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
chunk_split['line_length'] = np.array(lines)

If you're not using the --genome option you don't need to provide --transcript_fasta ../transcript_oligo.fasta, so the following command should be good:

xpore dataprep --eventalign nanopolish/psi0_transcrit_oligo.eventalign.txt --out_dir dataprep_results

Thanks!

Best wishes, Yuk Kei