def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
log.debug(opts)
output_names = dat.get_output_names(opts.data_files[0],
regex=opts.output_names)
stats = OrderedDict()
for name in output_names:
output = hdf.read(opts.data_files,
'outputs/%s' % name,
nb_sample=opts.nb_sample)
output = list(output.values())[0]
stats[name] = get_output_stats(output)
tmp = []
for key, value in six.iteritems(stats):
tmp.append(pd.DataFrame(value, index=[key]))
stats = pd.concat(tmp)
stats.index.name = 'output'
stats.reset_index(inplace=True)
print(stats.to_string())
if opts.out_tsv:
stats.to_csv(opts.out_tsv, sep='\t', index=False)
if opts.out_fig:
plot_stats(stats).savefig(opts.out_fig)
return 0
def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
log.debug(opts)
output_names = dat.get_output_names(opts.data_files[0],
regex=opts.output_names)
stats = OrderedDict()
for name in output_names:
output = hdf.read(opts.data_files, 'outputs/%s' % name,
nb_sample=opts.nb_sample)
output = list(output.values())[0]
stats[name] = get_output_stats(output)
tmp = []
for key, value in six.iteritems(stats):
tmp.append(pd.DataFrame(value, index=[key]))
stats = pd.concat(tmp)
stats.index.name = 'output'
stats.reset_index(inplace=True)
print(stats.to_string())
if opts.out_tsv:
stats.to_csv(opts.out_tsv, sep='\t', index=False)
if opts.out_fig:
plot_stats(stats).savefig(opts.out_fig)
return 0
def build_model(self):
opts = self.opts
log = self.log
output_names = dat.get_output_names(opts.train_files[0],
regex=opts.output_names,
nb_key=opts.nb_output)
if not output_names:
raise ValueError('No outputs found!')
dna_model = None
if opts.dna_model:
dna_model = self.build_dna_model()
cpg_model = None
if opts.cpg_model:
cpg_model = self.build_cpg_model()
if dna_model is not None and cpg_model is not None:
log.info('Joining models ...')
joint_model_builder = mod.joint.get(opts.joint_model)(
l1_decay=opts.l1_decay,
l2_decay=opts.l2_decay,
dropout=opts.dropout)
stem = joint_model_builder([dna_model, cpg_model])
stem.name = '_'.join([stem.name, dna_model.name, cpg_model.name])
elif dna_model is not None:
stem = dna_model
elif cpg_model is not None:
stem = cpg_model
else:
log.info('Loading existing model ...')
stem = mod.load_model(opts.model_files, log=log.info)
if sorted(output_names) == sorted(stem.output_names):
return stem
log.info('Removing existing output layers ...')
remove_outputs(stem)
outputs = mod.add_output_layers(stem.outputs, output_names)
model = Model(input=stem.inputs, output=outputs, name=stem.name)
return model
def build_model(self):
opts = self.opts
log = self.log
output_names = dat.get_output_names(opts.train_files[0],
regex=opts.output_names,
nb_key=opts.nb_output)
if not output_names:
raise ValueError('No outputs found!')
dna_model = None
if opts.dna_model:
dna_model = self.build_dna_model()
cpg_model = None
if opts.cpg_model:
cpg_model = self.build_cpg_model()
if dna_model is not None and cpg_model is not None:
log.info('Joining models ...')
joint_model_builder = mod.joint.get(opts.joint_model)(
l1_decay=opts.l1_decay,
l2_decay=opts.l2_decay,
dropout=opts.dropout)
stem = joint_model_builder([dna_model, cpg_model])
stem.name = '_'.join([stem.name, dna_model.name, cpg_model.name])
elif dna_model is not None:
stem = dna_model
elif cpg_model is not None:
stem = cpg_model
else:
log.info('Loading existing model ...')
stem = mod.load_model(opts.model_files, log=log.info)
if sorted(output_names) == sorted(stem.output_names):
return stem
log.info('Removing existing output layers ...')
remove_outputs(stem)
outputs = mod.add_output_layers(stem.outputs[0], output_names)
model = Model(inputs=stem.inputs, outputs=outputs, name=stem.name)
return model
def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
data_file = h5.File(opts.data_file, 'r')
nb_sample = len(data_file['pos'])
if opts.nb_sample:
nb_sample = min(nb_sample, opts.nb_sample)
data = dict()
for name in ['chromo', 'pos']:
data[name] = data_file[name][:nb_sample]
idx = None
if opts.chromos:
idx = np.in1d(data['chromo'],
[chromo.encode() for chromo in opts.chromos])
for key, value in six.iteritems(data):
data[key] = value[idx]
output_names = dat.get_output_names(opts.data_file,
regex=opts.output_names)
make_dir(opts.out_dir)
for output_name in output_names:
log.info(output_name)
data['output'] = data_file['outputs'][output_name][:nb_sample]
data['pred'] = data_file['preds'][output_name][:nb_sample]
if idx is not None:
for name in ['output', 'pred']:
data[name] = data[name][idx]
# Use `output` label if known, otherwise prediction
data['value'] = data['pred']
tmp = data['output'] != dat.CPG_NAN
data['value'][tmp] = data['output'][tmp]
name = output_name.split(dat.OUTPUT_SEP)
if name[0] == 'cpg':
name = name[-1]
else:
name = '_'.join(name)
out_file = os.path.join(opts.out_dir, name)
if opts.out_format == 'bedGraph':
write_to_bedGraph(data,
out_file + '.bedGraph.gz',
compression='gzip')
elif opts.out_format == 'hdf':
write_to_hdf(data, out_file + '.h5')
else:
tmp = 'Invalid output format "%s"!' % opts.out_format
raise ValueError()
log.info('Done!')
return 0
def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
log.debug(opts)
self.opts = opts
self.log = log
# Get performance curve functions from names.
curve_funs = dict()
if opts.curves:
for name in opts.curves:
curve_funs[name] = get_curve_fun(name)
anno_curve_funs = dict()
if opts.anno_curves:
for name in opts.anno_curves:
anno_curve_funs[name] = get_curve_fun(name)
log.info('Loading data ...')
# Read and sort predictions and outputs.
output_names = dat.get_output_names(opts.data_file,
regex=opts.output_names,
nb_key=opts.nb_output)
names = {'chromo': None, 'pos': None,
'outputs': output_names,
'preds': output_names}
data = hdf.read(opts.data_file, names, nb_sample=opts.nb_sample)
data['chromo'] = [chromo.decode() for chromo in data['chromo']]
data['chromo'] = np.array(data['chromo'])
data = fold_dict(data, nb_level=1)
idx = np.lexsort((data['pos'], data['chromo']))
data = slice_dict(data, idx)
for chromo in np.unique(data['chromo']):
chromo_pos = data['pos'][data['chromo'] == chromo]
tmp = np.sort(chromo_pos)
assert np.all(chromo_pos == tmp)
log.info('%d samples' % len(data['pos']))
reports = []
curves = []
log.info('Evaluating globally ...')
# Evaluate performances globally.
report = ev.evaluate_outputs(data['outputs'], data['preds'])
report['anno'] = ANNO_GLOBAL
reports.append(report)
pd.set_option('display.width', 1000)
print(ev.unstack_report(report))
if curve_funs:
# Performance curves.
for name, fun in curve_funs.items():
log.info('%s curve' % name)
curve = ev.evaluate_curve(data['outputs'], data['preds'],
fun=fun, nb_point=opts.nb_curve_point)
if curve is not None:
curve['curve'] = name
curve['anno'] = ANNO_GLOBAL
curves.append(curve)
if opts.anno_files:
log.info('Evaluating annotations ...')
# Evaluate annotations.
for anno_file in opts.anno_files:
anno = read_anno_file(anno_file)
anno_name = os.path.splitext(os.path.basename(anno_file))[0]
idx = annotate(data['chromo'], data['pos'], anno)
log.info('%s: %d' % (anno_name, idx.sum()))
if idx.sum() < opts.anno_min_sites:
log.info('Skipping due to insufficient annotated sites!')
continue
# Select data at annotated sites.
anno_data = slice_dict(data, idx)
report = ev.evaluate_outputs(anno_data['outputs'],
anno_data['preds'])
report['anno'] = anno_name
reports.append(report)
if curve_funs:
# Performance curves.
for name, fun in anno_curve_funs.items():
log.info('%s curve' % name)
curve = ev.evaluate_curve(
data['outputs'], data['preds'],
fun=fun, nb_point=opts.nb_curve_point)
if curve is not None:
curve['curve'] = name
curve['anno'] = anno_name
curves.append(curve)
make_dir(opts.out_dir)
if reports:
report = pd.concat(reports)
report = report[['anno', 'metric', 'output', 'value']]
self.save_report(report, 'metrics')
if curves:
curves = pd.concat(curves)
curves = curves[['anno', 'curve', 'output', 'x', 'y', 'thr']]
self.save_report(curves, 'curves')
log.info('Done!')
return 0
def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
data_file = h5.File(opts.data_file, 'r')
nb_sample = len(data_file['pos'])
if opts.nb_sample:
nb_sample = min(nb_sample, opts.nb_sample)
data = dict()
for name in ['chromo', 'pos']:
data[name] = data_file[name][:nb_sample]
idx = None
if opts.chromos:
idx = np.in1d(data['chromo'],
[chromo.encode() for chromo in opts.chromos])
for key, value in six.iteritems(data):
data[key] = value[idx]
output_names = dat.get_output_names(opts.data_file,
regex=opts.output_names)
make_dir(opts.out_dir)
for output_name in output_names:
log.info(output_name)
data['output'] = data_file['outputs'][output_name][:nb_sample]
data['pred'] = data_file['preds'][output_name][:nb_sample]
if idx is not None:
for name in ['output', 'pred']:
data[name] = data[name][idx]
# Use `output` label if known, otherwise prediction
data['value'] = data['pred']
tmp = data['output'] != dat.CPG_NAN
data['value'][tmp] = data['output'][tmp]
name = output_name.split(dat.OUTPUT_SEP)
if name[0] == 'cpg':
name = name[-1]
else:
name = '_'.join(name)
out_file = os.path.join(opts.out_dir, name)
if opts.out_format == 'bedGraph':
write_to_bedGraph(data, out_file + '.bedGraph.gz',
compression='gzip')
elif opts.out_format == 'hdf':
write_to_hdf(data, out_file + '.h5')
else:
tmp = 'Invalid output format "%s"!' % opts.out_format
raise ValueError()
log.info('Done!')
return 0
def main(self, name, opts):
logging.basicConfig(filename=opts.log_file,
format='%(levelname)s (%(asctime)s): %(message)s')
log = logging.getLogger(name)
if opts.verbose:
log.setLevel(logging.DEBUG)
else:
log.setLevel(logging.INFO)
log.debug(opts)
self.opts = opts
self.log = log
# Get performance curve functions from names.
curve_funs = dict()
if opts.curves:
for name in opts.curves:
curve_funs[name] = get_curve_fun(name)
anno_curve_funs = dict()
if opts.anno_curves:
for name in opts.anno_curves:
anno_curve_funs[name] = get_curve_fun(name)
log.info('Loading data ...')
# Read and sort predictions and outputs.
output_names = dat.get_output_names(opts.data_file,
regex=opts.output_names,
nb_key=opts.nb_output)
names = {
'chromo': None,
'pos': None,
'outputs': output_names,
'preds': output_names
}
data = hdf.read(opts.data_file, names, nb_sample=opts.nb_sample)
data['chromo'] = [chromo.decode() for chromo in data['chromo']]
data['chromo'] = np.array(data['chromo'])
data = fold_dict(data, nb_level=1)
idx = np.lexsort((data['pos'], data['chromo']))
data = slice_dict(data, idx)
for chromo in np.unique(data['chromo']):
chromo_pos = data['pos'][data['chromo'] == chromo]
tmp = np.sort(chromo_pos)
assert np.all(chromo_pos == tmp)
log.info('%d samples' % len(data['pos']))
reports = []
curves = []
log.info('Evaluating globally ...')
# Evaluate performances globally.
report = ev.evaluate_outputs(data['outputs'], data['preds'])
report['anno'] = ANNO_GLOBAL
reports.append(report)
pd.set_option('display.width', 1000)
print(ev.unstack_report(report))
if curve_funs:
# Performance curves.
for name, fun in curve_funs.items():
log.info('%s curve' % name)
curve = ev.evaluate_curve(data['outputs'],
data['preds'],
fun=fun,
nb_point=opts.nb_curve_point)
if curve is not None:
curve['curve'] = name
curve['anno'] = ANNO_GLOBAL
curves.append(curve)
if opts.anno_files:
log.info('Evaluating annotations ...')
# Evaluate annotations.
for anno_file in opts.anno_files:
anno = read_anno_file(anno_file)
anno_name = os.path.splitext(os.path.basename(anno_file))[0]
idx = annotate(data['chromo'], data['pos'], anno)
log.info('%s: %d' % (anno_name, idx.sum()))
if idx.sum() < opts.anno_min_sites:
log.info('Skipping due to insufficient annotated sites!')
continue
# Select data at annotated sites.
anno_data = slice_dict(data, idx)
report = ev.evaluate_outputs(anno_data['outputs'],
anno_data['preds'])
report['anno'] = anno_name
reports.append(report)
if curve_funs:
# Performance curves.
for name, fun in anno_curve_funs.items():
log.info('%s curve' % name)
curve = ev.evaluate_curve(data['outputs'],
data['preds'],
fun=fun,
nb_point=opts.nb_curve_point)
if curve is not None:
curve['curve'] = name
curve['anno'] = anno_name
curves.append(curve)
make_dir(opts.out_dir)
if reports:
report = pd.concat(reports)
report = report[['anno', 'metric', 'output', 'value']]
self.save_report(report, 'metrics')
if curves:
curves = pd.concat(curves)
curves = curves[['anno', 'curve', 'output', 'x', 'y', 'thr']]
self.save_report(curves, 'curves')
log.info('Done!')
return 0