def calculate_distances(self, peptides):
import sys
print "@@@", sys.getrecursionlimit()
dd = self.__d2s.getDistance2Self(p2s(peptides), self.__max_res)
print "derp"
result = {key: value.values() for key, value in dd.iteritems()}
# create temporary file with peptides for distance computation
resultDf = Distance2SelfResult.from_dict(result)
resultDf['matrix'] = self.__matrix.name
return resultDf
def parse_external_result(self, result):
"""
:rtype : DataFrame
"""
parsedResult = {}
for line in result.strip().split('\n'):
splitted = line.strip().split(" ")[-1].split(";")
distanceValues = []
peptide = splitted[0].split(":")[0]
for s in splitted[:-1]:
distanceValues.append(float(s.split(",")[-1]))
parsedResult[peptide] = distanceValues
resultDf = Distance2SelfResult.from_dict(parsedResult)
resultDf['trie'] = self.__trie.split('/')[-1]
resultDf['matrix'] = self.__matrix.path_to_matrix_file.split('/')[-1]
return resultDf
