Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
HMM Class Reference

Public Member Functions

def __init__ (self, signature="", sequences=dict(), db_path="", output_path="", aligner="clustal", num_cores=4)
 
def __check_aligner_in_path__ (self, aligner)
 
def __which_exec__ (self, name)
 
def __init_tmp_files__ (self)
 
def run (self)
 
def parse (self, hmm_results_file_name)
 
def __build_hmm__ (self)
 
def __query_db__ (self)
 
def __parse_hmm_results__ (self)
 
def __clean_up__ (self)
 
def get_results (self, threshold)
 
def get_results_with_e_value (self, threshold)
 

Public Attributes

 signature
 

Detailed Description

HMM wrapper class.

HMM wrapper class.

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  signature = "",
  sequences = dict(),
  db_path = "",
  output_path = "",
  aligner = "clustal",
  num_cores = 4 
)

Member Function Documentation

◆ __build_hmm__()

def __build_hmm__ (   self)

◆ __check_aligner_in_path__()

def __check_aligner_in_path__ (   self,
  aligner 
)

◆ __clean_up__()

def __clean_up__ (   self)

◆ __init_tmp_files__()

def __init_tmp_files__ (   self)

◆ __parse_hmm_results__()

def __parse_hmm_results__ (   self)

◆ __query_db__()

def __query_db__ (   self)

◆ __which_exec__()

def __which_exec__ (   self,
  name 
)

◆ get_results()

def get_results (   self,
  threshold 
)

◆ get_results_with_e_value()

def get_results_with_e_value (   self,
  threshold 
)

◆ parse()

def parse (   self,
  hmm_results_file_name 
)

◆ run()

def run (   self)

Member Data Documentation

◆ signature

signature