def run_hmmbuild(self):

        '''
        Generate hmm with hhbuild,
        output to file. Also stores query names.
        '''

        for alignment in self.alignment_list:

            print 'building Hmm for', alignment

            alignment_full_path = self.alignment_dir + alignment
            query_name = alignment.split("_")[0]
            self.query_names.append(query_name)

            new_hmm= self.hmm_dir + query_name + ".hmm"

            hmmbuild_output = subprocess.call(["hmmbuild", new_hmm,
             alignment_full_path])

        print 'hhbuild complete for', self.query_names
def run_hmmbuild ( self ) : for alignment in self . alignment_list : print 'building Hmm for' , alignment alignment_full_path = self . alignment_dir + alignment query_name = alignment . split ( "_" ) [ 0 ] self . query_names . append ( query_name ) new_hmm = self . hmm_dir + query_name + ".hmm" hmmbuild_output = subprocess . call ( [ "hmmbuild" , new_hmm , alignment_full_path ] ) print 'hhbuild complete for' , self . query_names
Generate hmm with hhbuild,
        output to file. Also stores query names.