yuukiiwa
commented
2 years ago Hi @zzf77,
The most updated version of xpore (v2.1) no longer has the --summary command, so it will be great if you can update xpore to v2.1.
Thank you!
Best wishes, Yuk Kei
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. When I came to the step of dataprep following the help and manual, I kept getting the same ERROR and could not proceed. My working directory: ~/demo/data/HEK293T-METTL3-KO-rep1
Using the command "xpore-dataprep -h" we can see the usage information, which tell us the "summary" is required: (apptest) [zzf@ser1 ~]$ xpore-dataprep -h usage: xpore-dataprep [-h] --eventalign EVENTALIGN --summary SUMMARY --out_dir OUT_DIR [--ensembl ENSEMBL] [--species SPECIES] [--genome] [--n_processes N_PROCESSES] [--readcount_max READCOUNT_MAX] [--resume]
While in https://xpore.readthedocs.io/en/latest/quickstart.html, i don't see the "summary" command.
The running command: xpore-dataprep \ --eventalign /home/dragon/Database/zzf/demo/demo/data/HEK293T-METTL3-KO-rep1/nanopolish/eventalign.txt \ --summary /home/dragon/Database/zzf/demo/demo/data/HEK293T-METTL3-KO-rep1/nanopolish/summary.txt \ --gtf_or_gff /home/dragon/Database/zzf/demo/demo/demo.gtf \ --transcript_fasta /home/dragon/Database/zzf/demo/demo/demo.fa \ --out_dir dataprep \ --genome
And then came this ERROR: xpore-dataprep: error: unrecognized arguments: --gtf_or_gff /home/dragon/Database/zzf/demo/demo/demo.gtf --transcript_fasta /home/dragon/Database/zzf/demo/demo/demo.fa
If i use "xpore dataprep', the tool will come with this： Command 'xpore' not found,did you mean:
It would be grateful if you could give me some advice on solving this problem. Thanks for developing this nice tool.