create folder and save file inside each new folder

Question

[marcela.uliano]

Hi all, I apologize in advance. I feel this is simple but I'm stuck for a few hours.

Giving a list of gene names(list_of_genes) and a tab delimited file such as id"\t"gene_names (args.i bellow),

how do I create a folder with gene name and save selected id within each new folder. So I guess its basically creating a folder g and then save the two instances of df5 data frame within this new g.

I'm at:

list_of_genes =['lactato desi', 'NADH lac']
for g in list_of_genes:
        m=['id', 'all']
        ids_tabbed=pd.read_csv(args.i,  sep="\t", names=m)
        df5 = ids_tabbed[ids_tabbed['all'].str.contains(g, na=False)]
        os.mkdir('{}'.format(str(g.replace(' ', '_'))))
        df5.to_csv(f"{g.replace(' ', '_')}.csv", index=False, header=None, sep="\t")
        df5[['id']].to_csv(f"ID.{g.replace(' ', '_')}.id.csv", index=False, header=None)

Im able to create the folders: lactato_desi NADH_lac and the files. But I don't know how to save each bunch files to its specific folder =(

Real thanks for your help!

Answer 1

[LChart]

Provide the local path to the file:

dir_name = g.replace(' ', '_')
file_name = g.replace(' ', '_') + '.csv'
file_path = '{}/{}'.format(dir_name, file_name)
os.mkdir(dir_name)
df5.to_csv(file_path)

[marcela.uliano]

All working. Thanks a lot =)

[Ram]

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[marcela.uliano]

Noted. Thank Ram