ipyrad/core/assembly.py
def _step5func(self, samples, force, ipyclient):
        """ hidden wrapped function to start step 5 """
        ## print header
        if self._headers:
            print("\n  Step 5: Consensus base calling ")

        ## Get sample objects from list of strings
        samples = _get_samples(self, samples)

        ## Check if all/none in the right state
        if not self._samples_precheck(samples, 5, force):
            raise IPyradError(FIRST_RUN_4)

        elif not force:
            ## skip if all are finished
            if all([i.stats.state >= 5 for i in samples]):
                print(CONSENS_EXIST.format(len(samples)))
                return
        ## pass samples to rawedit
        assemble.consens_se.run(self, samples, force, ipyclient)
def _step5func(self, samples, force, ipyclient):
        """ hidden wrapped function to start step 5 """
        ## print header
        if self._headers:
            print("\n  Step 5: Consensus base calling ")

        ## Get sample objects from list of strings
        samples = _get_samples(self, samples)

        ## Check if all/none in the right state
        if not self._samples_precheck(samples, 5, force):
            raise IPyradError(FIRST_RUN_4)

        elif not force:
            ## skip if all are finished
            if all([i.stats.state >= 5 for i in samples]):
                print(CONSENS_EXIST.format(len(samples)))
                return
        ## pass samples to rawedit
        assemble.consens_se.run(self, samples, force, ipyclient)
def _step5func ( self , samples , force , ipyclient ) : ## print header if self . _headers : print ( "\n  Step 5: Consensus base calling " ) ## Get sample objects from list of strings samples = _get_samples ( self , samples ) ## Check if all/none in the right state if not self . _samples_precheck ( samples , 5 , force ) : raise IPyradError ( FIRST_RUN_4 ) elif not force : ## skip if all are finished if all ( [ i . stats . state >= 5 for i in samples ] ) : print ( CONSENS_EXIST . format ( len ( samples ) ) ) return ## pass samples to rawedit assemble . consens_se . run ( self , samples , force , ipyclient )
hidden wrapped function to start step 5
hidden wrapped function to start step 5