title: Python; write dataframe output to different subdirectories
body: <p>I am running my script from my current working directory. With my script, I loop over the subdirectories of the current working directory. Each subdirectory contains the 3 files mentioned in the script, and for each subdirectory, I merge the 3 files to one dataframe. As my script is now, it writes the merged dataframe of only one subdirectory to the current working directory. What I want is the csv file with the merged dataframe of each subdirectory saved in that subdirectory, or a file with dataframes of each subdirectory concatenated to one large output file.
  With my script, I have only the output of one subdirectory in the output file.</p>
  
  <p>My script is as follows:</p>
  
  <pre><code>print('Start merging contig files')
  
  for root, dirs, files in os.walk(os.getcwd()):
      filepath = os.path.join(root, 'genes.faa.genespercontig.csv')
      if os.path.isfile(filepath):
          with open(filepath, 'r') as f1:
              df1 = pd.read_csv(f1, header=None, delim_whitespace=True, names = ["contig", "genes"])
              df1['genome'] = os.path.basename(os.path.dirname(filepath))
  
      filepath = os.path.join(root, 'hmmer.analyze.txt.results.txt')
      if os.path.isfile(filepath):
          with open(filepath, 'r') as f2:
              df2 = pd.read_csv(f2, header=None, delim_whitespace=True, names = ["contig", "SCM"])
              df2['genome'] = os.path.basename(os.path.dirname(filepath))
  
      filepath = os.path.join(root, 'genes.fna.output_blastplasmiddb.out.count_plasmiddbhit.out')
      if os.path.isfile(filepath):
          with open(filepath, 'r') as f3:
              df3 = pd.read_csv(f3, header=None, delim_whitespace=True, names = ["contig", "plasmid_genes"])
              df3['genome'] = os.path.basename(os.path.dirname(filepath))
  
  #merge dataframes
  dfmerge1 = pd.merge(df1, df2, on=['genome', 'contig'], how='outer')
  df_end = pd.merge(dfmerge1, df3, on=['genome', 'contig'], how='outer')      
  
  df_end.to_csv('outputgenesdf.csv')
  </code></pre>