def get_consensi_tree_filename(self, region, format='newick'): '''Get the filename of the consensi tree of the patient''' from hivwholeseq.patients.filenames import get_consensi_tree_filename return get_consensi_tree_filename(self.name, region, format=format)
a.calc_ancestral_sequences() a.cleanup_tree() if VERBOSE >= 2: print 'Annotate tree' annotate_tree_all(tree, seqs_all, VERBOSE=VERBOSE) if VERBOSE >= 2: print 'Ladderize tree' tree.ladderize() correct_minimal_branches(tree) if use_save: if VERBOSE >= 2: print 'Save tree (JSON)' reg_tmp = '_'.join(pcodes)+'_'+region fn = get_consensi_tree_filename('all', reg_tmp, format='json') tree_json = tree_to_json(tree.root, fields=('DSI', 'patient', 'sequence', 'muts', 'VL', 'CD4', 'subtype', 'confidence'), ) write_json(tree_json, fn, indent=1)
a = ancestral_sequences(tree, ali_all, alphabet='ACGT-N', copy_tree=False, attrname='sequence', seqtype='str') a.calc_ancestral_sequences() a.cleanup_tree() if VERBOSE >= 2: print 'Annotate tree' annotate_tree_all(tree, seqs_all, VERBOSE=VERBOSE) if VERBOSE >= 2: print 'Ladderize tree' tree.ladderize() correct_minimal_branches(tree) if use_save: if VERBOSE >= 2: print 'Save tree (JSON)' reg_tmp = '_'.join(pcodes) + '_' + region fn = get_consensi_tree_filename('all', reg_tmp, format='json') tree_json = tree_to_json( tree.root, fields=('DSI', 'patient', 'sequence', 'muts', 'VL', 'CD4', 'subtype', 'confidence'), ) write_json(tree_json, fn, indent=1)