ind=datum['ind'],
times=datum['times'],
seqs=datum['seqs'],
ali=datum['alim'],
)
if VERBOSE >= 2:
print 'Build tree'
times = datum['times']
alim = datum['alim']
hct = datum['hct']
hft = 1.0 * hct / hct.sum(axis=0)
ali = expand_annotate_alignment(alim, hft, hct, times,
freqmin=freqmin,
VERBOSE=VERBOSE)
tree = build_tree_fasttree(ali, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Infer ancestral sequences'
a = ancestral_sequences(tree, ali, 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_time_freq_count(tree, ali)
annotate_tree(patient, tree, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Ladderize tree'
for region in regionspat:
if VERBOSE >= 1:
print pname, region
if VERBOSE == 1:
print ''
if VERBOSE >= 2:
print 'Get alignment'
ali = patient.get_consensi_alignment(region)
if VERBOSE >= 2:
print 'Build tree'
sys.stdout.flush()
tree = build_tree_fasttree(ali, rootname=ali[0].id,
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Infer ancestral sequences'
a = ancestral_sequences(tree, ali, alphabet='ACGT-N', copy_tree=False,
attrname='sequence', seqtype='str')
a.calc_ancestral_sequences()
a.cleanup_tree()
if VERBOSE >= 2:
print 'Annotate tree'
fields = ['DSI', 'muts', 'VL', 'ntemplates', 'CD4', 'subtype']
if region in regionsprot:
fields.append('mutsprot')
for region in regions:
if VERBOSE >= 1:
print region
if use_save:
if VERBOSE >= 2:
print 'Get alignment'
ali = get_subtype_reference_alignment(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Calculate tree'
tree = build_tree_fasttree(ali, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Save to file, newick'
fn_out = get_subtype_reference_alignment_tree_filename(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE,
format='newick')
Phylo.write([tree], fn_out, 'newick')
if VERBOSE >= 2:
print 'Annotate tree (for JSON format)'
for region in regionspat:
if VERBOSE >= 1:
print pname, region
if VERBOSE == 1:
print ''
if VERBOSE >= 2:
print 'Get alignment'
ali = patient.get_consensi_alignment(region)
if VERBOSE >= 2:
print 'Build tree'
sys.stdout.flush()
tree = build_tree_fasttree(ali,
rootname=ali[0].id,
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Infer ancestral sequences'
a = ancestral_sequences(tree,
ali,
alphabet='ACGT-N',
copy_tree=False,
attrname='sequence',
seqtype='str')
a.calc_ancestral_sequences()
a.cleanup_tree()
if VERBOSE >= 2:
print 'Annotate tree'
