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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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SampCompDB error #207

Open rezarahman12 opened 2 years ago

rezarahman12 commented 2 years ago

Dear Nanocomopore team, Thanks again for this wonderful tool. I have tried loading the nanocomopore SampComp output file outSampComp.db.dat Below is my code-

Load database

db = SampCompDB ( db_fn = "/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/outSampComp.db", fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa")

save the results

Reload DB

db = SampCompDB (db_fn = "/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/outSampComp.db", fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa", log_level="warning")

Save report

db.save_report (output_fn="/scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep/nanocompore_report.tsv")

the log file is given below- 2022-11-01 15:49:07.853 | INFO | nanocompore.SampCompDB:init:55 - Loading SampCompDB 2022-11-01 15:49:07.891 | DEBUG | nanocompore.SampCompDB:init:62 - Reading Metadata 2022-11-01 15:49:07.906 | DEBUG | nanocompore.SampCompDB:init:68 - Loading list of reference ids 2022-11-01 15:49:07.915 | DEBUG | nanocompore.SampCompDB:init:82 - Checking files and arg values 2022-11-01 15:49:07.935 | INFO | nanocompore.SampCompDB:init:100 - Calculate results Traceback (most recent call last): File "nanocomopore_sampcompdb.py", line 26, in fasta_fn = "/scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa", log_level="warning") TypeError: init() got an unexpected keyword argument 'log_level'

Could you please tell me how to fix this problem?

Kind regards Reza

lmulroney commented 1 year ago

Dear rezarahman12,

Ttry again but after removeing: , log_level="warning" from your db instantiating line.

Logan