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)
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)
