problem with initializeScenic()

[Mancang-Yu]

Hi,I have some trouble with initializeScenic().I download the file from this site(https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/). But I find the file names have some differences with the required file name. So I rename the files. When I run initializeScenic(), I got an error"Error in eval(as.name(motifAnnotName)): can't fine the object 'motifAnnotations_mgi'".Is there something wrong?

[basetwin]

Hi,

I’ve encountered a similar problem before, and in my case, it was caused by a mismatch between the predicted file format (older version) and the new database file format. Specifically, the older format had a feature column as the first column, while the newer database format uses a motif column, which appears as the last column.

To resolve this, I renamed the motif column to feature and moved it to be the first column. This adjustment aligned the file with the expected format and resolved the issue for me.

I hope this helps! Let me know if you need further clarification.

like this code

dir = input('Please enter the directory of files which you want to change: ')
#dir = '/gpfs/home2/sbjs0428/tutorial/R/scenic_heochan/cisTarget_databases'

for file in os.listdir(dir):
    if file.endswith('feather'):
        name = file
        df = pd.read_feather(file)
        df = df.rename(columns={'motifs':'features'})
        columns = ['features'] + [col for col in df.columns if col != 'features']
        df = df[columns]
        df.to_feather(name)