def _step3func(self, samples, noreverse, maxindels, force, ipyclient):
        """ hidden wrapped function to start step 3 """
        ## print headers
        if self._headers:
            print("\n  Step 3: Clustering/Mapping reads")

        ## Require reference seq for reference-based methods
        if self.paramsdict['assembly_method'] != "denovo":
            if not self.paramsdict['reference_sequence']:
                raise IPyradError(REQUIRE_REFERENCE_PATH\
                            .format(self.paramsdict["assembly_method"]))
            else:
                ## index the reference sequence
                ## Allow force to reindex the reference sequence
                ## send to run on the cluster. 
                lbview = ipyclient.load_balanced_view()
                async = lbview.apply(index_reference_sequence, *(self, force))

                ## print a progress bar for the indexing
                start = time.time()
                while 1:
                    elapsed = datetime.timedelta(seconds=int(time.time()-start))
                    printstr = " {}    | {} | s3 |".format("indexing reference", elapsed)
                    finished = int(async.ready())
                    progressbar(1, finished, printstr, spacer=self._spacer)
                    if finished:
                        print("")
                        break
                    time.sleep(0.9)
                ## error check
                if not async.successful():
                    raise IPyradWarningExit(async.result())

        ## 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, 3, force):
            raise IPyradError(FIRST_RUN_2)

        elif not force:
            ## skip if all are finished
            if all([i.stats.state >= 3 for i in samples]):
                print(CLUSTERS_EXIST.format(len(samples)))
                return

        ## run the step function
        assemble.cluster_within.run(self, samples, noreverse, maxindels,
                                    force, ipyclient)
def _step3func(self, samples, noreverse, maxindels, force, ipyclient):
        """ hidden wrapped function to start step 3 """
        ## print headers
        if self._headers:
            print("\n  Step 3: Clustering/Mapping reads")

        ## Require reference seq for reference-based methods
        if self.paramsdict['assembly_method'] != "denovo":
            if not self.paramsdict['reference_sequence']:
                raise IPyradError(REQUIRE_REFERENCE_PATH\
                            .format(self.paramsdict["assembly_method"]))
            else:
                ## index the reference sequence
                ## Allow force to reindex the reference sequence
                ## send to run on the cluster. 
                lbview = ipyclient.load_balanced_view()
                async = lbview.apply(index_reference_sequence, *(self, force))

                ## print a progress bar for the indexing
                start = time.time()
                while 1:
                    elapsed = datetime.timedelta(seconds=int(time.time()-start))
                    printstr = " {}    | {} | s3 |".format("indexing reference", elapsed)
                    finished = int(async.ready())
                    progressbar(1, finished, printstr, spacer=self._spacer)
                    if finished:
                        print("")
                        break
                    time.sleep(0.9)
                ## error check
                if not async.successful():
                    raise IPyradWarningExit(async.result())

        ## 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, 3, force):
            raise IPyradError(FIRST_RUN_2)

        elif not force:
            ## skip if all are finished
            if all([i.stats.state >= 3 for i in samples]):
                print(CLUSTERS_EXIST.format(len(samples)))
                return

        ## run the step function
        assemble.cluster_within.run(self, samples, noreverse, maxindels,
                                    force, ipyclient)
def _step3func ( self , samples , noreverse , maxindels , force , ipyclient ) : ## print headers if self . _headers : print ( "\n  Step 3: Clustering/Mapping reads" ) ## Require reference seq for reference-based methods if self . paramsdict [ 'assembly_method' ] != "denovo" : if not self . paramsdict [ 'reference_sequence' ] : raise IPyradError ( REQUIRE_REFERENCE_PATH . format ( self . paramsdict [ "assembly_method" ] ) ) else : ## index the reference sequence ## Allow force to reindex the reference sequence ## send to run on the cluster.  lbview = ipyclient . load_balanced_view ( ) async = lbview . apply ( index_reference_sequence , * ( self , force ) ) ## print a progress bar for the indexing start = time . time ( ) while 1 : elapsed = datetime . timedelta ( seconds = int ( time . time ( ) - start ) ) printstr = " {}    | {} | s3 |" . format ( "indexing reference" , elapsed ) finished = int ( async . ready ( ) ) progressbar ( 1 , finished , printstr , spacer = self . _spacer ) if finished : print ( "" ) break time . sleep ( 0.9 ) ## error check if not async . successful ( ) : raise IPyradWarningExit ( async . result ( ) ) ## 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 , 3 , force ) : raise IPyradError ( FIRST_RUN_2 ) elif not force : ## skip if all are finished if all ( [ i . stats . state >= 3 for i in samples ] ) : print ( CLUSTERS_EXIST . format ( len ( samples ) ) ) return ## run the step function assemble . cluster_within . run ( self , samples , noreverse , maxindels , force , ipyclient )
hidden wrapped function to start step 3
hidden wrapped function to start step 3