old_contents: #!/usr/bin/env python
  
  
  def select_taxids(species, reference_taxonomy_file, selected_taxonomy_file):
      '''Selects taxonomy ids for the query species'''
      if not str(species) == 'None':
          parse_uniprot_tax_file(
              species, reference_taxonomy_file, selected_taxonomy_file)
      else:
          parse_uniprot_tax_file(
              'N=', reference_taxonomy_file, selected_taxonomy_file)
  
          
  def parse_uniprot_tax_file(
          species, reference_taxonomy_file, selected_taxonomy_file):
      '''Parses the taxonomy id file from UniProt for all the species'''
      with open(selected_taxonomy_file, 'w') as out_fh:
          out_fh.write("Official (scientific) name\tTaxonomy ID\n")
          with open(reference_taxonomy_file, 'r') as in_fh:
              for entry in in_fh:
                  if 'N=' in entry:
                      if ',' in species:
                          for each_species in species.split(','):
                              if each_species.lower() in entry.lower():
                                  tax_id = entry.split(':')[0].split(' ')[-1]
                                  species_name = entry.strip().split('=')[1]
                                  out_fh.write("%s\t%s\n" % (
                                      species_name, tax_id))
                      else:
                          if species.lower() in entry.lower():
                              tax_id = entry.split(':')[0].split(' ')[-1]
                              species_name = entry.strip().split('=')[1]
                              out_fh.write("%s\t%s\n" % (species_name, tax_id))
  
new_contents: #!/usr/bin/env python
  # Description = Download the taxonomy ids related to user provided species
  # author= "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  # email = "malvika.sharan@uni-wuerzburg.de"
  # 2016-05-20
  
  def select_taxids(species, reference_taxonomy_file, selected_taxonomy_file):
      '''Selects taxonomy ids for the query species'''
      if not str(species) == 'None':
          parse_uniprot_tax_file(
              species, reference_taxonomy_file, selected_taxonomy_file)
      else:
          parse_uniprot_tax_file(
              'N=', reference_taxonomy_file, selected_taxonomy_file)
  
          
  def parse_uniprot_tax_file(
          species, reference_taxonomy_file, selected_taxonomy_file):
      '''Parses the taxonomy id file from UniProt for all the species'''
      with open(selected_taxonomy_file, 'w') as out_fh:
          out_fh.write("Official (scientific) name\tTaxonomy ID\n")
          with open(reference_taxonomy_file, 'r') as in_fh:
              for entry in in_fh:
                  if 'N=' in entry:
                      if ',' in species:
                          for each_species in species.split(','):
                              if each_species.lower() in entry.lower():
                                  tax_id = entry.split(':')[0].split(' ')[-1]
                                  species_name = entry.strip().split('=')[1]
                                  out_fh.write("%s\t%s\n" % (
                                      species_name, tax_id))
                      else:
                          if species.lower() in entry.lower():
                              tax_id = entry.split(':')[0].split(' ')[-1]
                              species_name = entry.strip().split('=')[1]
                              out_fh.write("%s\t%s\n" % (species_name, tax_id))
  
subject: Update uniprot_taxid.py