import pandas as pd f = pd.read_csv('IFIS_site_id.txt',sep='\t') ids = f.site_id #ids = ids[1:len(ids)-1] for site in ids: filename = '%s.txt' % (site) f = pd.read_table(filename,sep='\t',skip_blank_lines=True,comment='#',index_col=0) test = f[len(f):None:-1] test.to_csv(filename,sep='\t',index=False)