def get_rsat_organism(self, kegg_organism):
"""returns the HTML page for the directory listing"""
logging.debug('RSAT - get_directory()')
cache_file = "/".join([self.cache_dir, 'rsat_dir.html'])
text = util.read_url_cached("/".join([self.base_url, RsatDatabase.DIR_PATH]),
cache_file).decode('utf-8')
suggestion1 = util.best_matching_links(self.kegg_species, text)[0].rstrip('/')
suggestion2 = util.best_matching_links(kegg_organism, text)[0].rstrip('/')
if suggestion1 != suggestion2:
ncbi_code1 = self.__get_ncbi_code(suggestion1)
ncbi_code2 = self.__get_ncbi_code(suggestion2)
if str(ncbi_code1) == str(self.ncbi_code):
return suggestion1
elif str(ncbi_code2) == str(self.ncbi_code):
return suggestion2
else:
logging.warn("can't find the correct RSAT mapping !")
return suggestion1
else:
ncbi_code = self.__get_ncbi_code(suggestion1)
if str(ncbi_code) == str(self.ncbi_code):
return suggestion1
else:
logging.warn("can't find the correct RSAT mapping !")
return suggestion1
def get_rsat_organism(self, kegg_organism):
"""returns the HTML page for the directory listing"""
logging.debug('RSAT - get_directory()')
cache_file = "/".join([self.cache_dir, 'rsat_dir.html'])
text = util.read_url_cached("/".join([self.base_url, RsatDatabase.DIR_PATH]),
cache_file).decode('utf-8')
suggestion1 = util.best_matching_links(self.kegg_species, text)[0].rstrip('/')
suggestion2 = util.best_matching_links(kegg_organism, text)[0].rstrip('/')
if suggestion1 != suggestion2:
ncbi_code1 = self.__get_ncbi_code(suggestion1)
ncbi_code2 = self.__get_ncbi_code(suggestion2)
if str(ncbi_code1) == str(self.ncbi_code):
return suggestion1
elif str(ncbi_code2) == str(self.ncbi_code):
return suggestion2
else:
logging.warn("can't find the correct RSAT mapping !")
return suggestion1
else:
ncbi_code = self.__get_ncbi_code(suggestion1)
if str(ncbi_code) == str(self.ncbi_code):
return suggestion1
else:
logging.warn("can't find the correct RSAT mapping !")
return suggestion1
def test_best_rsat_matches(self):
"""test the best_matching_links function"""
with open(RSAT_LIST_FILE_PATH) as inputfile:
html = inputfile.read()
matches = util.best_matching_links('Halobacterium', html)
self.assertEquals("Halobacterium_sp/", matches[0])
def test_best_rsat_matches(self):
"""test the best_matching_links function"""
with open(RSAT_LIST_FILE_PATH) as inputfile:
html = inputfile.read()
matches = util.best_matching_links('Halobacterium', html)
self.assertEquals("Halobacterium_sp/", matches[0])
