def save(self, step):
print(color_text('Saving models ...', 'green'))
torch.save(
self.model.module.state_dict(),
os.path.join(self.args.save_path, 'model',
'pred_model_%09d.pt' % step))
torch.save(
self.optim.state_dict(),
os.path.join(self.args.save_path, 'optimizer', 'optimizer.pt'))
with open(os.path.join(self.args.save_path, 'epoch.pkl'), 'wb') as f:
pkl.dump(self.epoch, f)
self.bmanager.save_spc_buffer()
print(color_text('Model saved successfully!', 'green'))
def __str__(self):
"""c
"""
print_var = ' '
if self.is_terminal:
print_var = self.char + print_var
if self.char == self.PLUS:
print_var = color_text(print_var, "green")
else:
print_var = color_text(print_var, "red")
elif self.is_invalid():
print_var = color_text(self.char + print_var, "yellow")
else:
action = self.utility[1]
print_var = ACTION_CHARS[action] + print_var
return print_var
def write_job(analydir, jobname, jobs, orders):
job_dir = os.path.join(analydir, 'job')
log_dir = os.path.join(analydir, 'log', jobname)
create_dir(job_dir)
create_dir(log_dir)
log_path = os.path.join(job_dir, jobname)
with open(log_path, 'w') as log:
# write jobs
for job in jobs:
job_part = '''\
job_begin
name {name}
memory {memory}
status {status}
sched_options {sched}
cmd_begin
{cmd}
cmd_end
job_end\n
'''.format(**job)
log.write(textwrap.dedent(job_part))
# write orders
for order in orders:
log.write(order + '\n')
# write log_dir
log.write('\nlog_dir %s\n' % log_dir)
print 'successfully generated job, and you can start with: %s' % utils.color_text(
'sjm job/' + jobname, 'green', style='bright')
def train_guide_action(self, step):
if self.bmanager.spc_buffer.can_sample_guide(self.bsize):
obs, guide_action = self.bmanager.spc_buffer.sample_guide(
self.bsize)
q = self.model(obs, action_only=True)
loss = self.guide_loss_func()(q, guide_action)
print('Guidance loss %0.4f' % loss.data.cpu().numpy())
return loss
else:
print(
color_text('Insufficient expert data for imitation learning.',
'red'))
return 0.0
def __init__(self, parent=None, name: str = '', description: str = ''):
super(Dialog, self).__init__(parent)
self.option = QSpinBox()
self.option.setMinimum(5)
self.option.setMaximum(10000000)
self.option.setValue(300)
self.setWindowTitle('Get giles')
self.label = QLabel(color_text('Insert option:', 'limegreen'))
self.name_label = QLabel(color_text(name + ':', 'limegreen'))
self.tooltip = QLabel(description)
self.ok_button = QPushButton('Ok', self)
self.ok_button.setFixedSize(self.ok_button.sizeHint())
self.ok_button.clicked.connect(self.accept)
self.cancel_button = QPushButton('Cancel', self)
self.cancel_button.setFixedSize(self.cancel_button.sizeHint())
self.cancel_button.clicked.connect(self.reject)
layout = QGridLayout(self)
layout.addWidget(self.name_label, 0, 0, 1, 3)
layout.addWidget(self.tooltip, 1, 0, 1, 3)
layout.addWidget(self.label, 2, 0, 1, 3)
layout.addWidget(self.option, 3, 0, 1, 3)
layout.setColumnStretch(0, 1)
layout.setColumnStretch(1, 0)
layout.setColumnStretch(2, 0)
layout.addWidget(self.ok_button, 4, 1)
layout.addWidget(self.cancel_button, 4, 2)
self.setFixedHeight(self.sizeHint().height())
self.setFixedWidth(self.sizeHint().width())
self.option.setFocus()
def __init__(self, head_channels, classes, snapshot_file='model.pth.tar'):
super(SegmentationModule, self).__init__()
norm_act = partial(ABN, activation="leaky_relu", slope=.01)
self.body = models.__dict__["net_wider_resnet38_a2"](norm_act=norm_act, dilation=(1, 2, 4, 4))
self.head = DeeplabV3(4096, 256, 256, norm_act=norm_act, pooling_size=(84, 84))
self.cls = nn.Conv2d(head_channels, classes, 1)
self.transform = SegmentationTransform(
2048,
(0.41738699, 0.45732192, 0.46886091),
(0.25685097, 0.26509955, 0.29067996),
)
dir_path = os.path.dirname(os.path.realpath(__file__))
snapshot_file = os.path.join(dir_path, snapshot_file)
if snapshot_file is not None:
if not os.path.exists(snapshot_file):
print(color_text('No local model found at {}'.format(snapshot_file), 'red'))
print(color_text('Please download pretrained model from https://drive.google.com/file/d/1SJJx5-LFG3J3M99TrPMU-z6ZmgWynxo-/view', 'red'))
data = torch.load(snapshot_file)
self.body.load_state_dict(data["state_dict"]["body"])
self.head.load_state_dict(data["state_dict"]["head"])
self.cls.load_state_dict(data["state_dict"]["cls"])
print('Loading segmentation model from %s' % snapshot_file)
def train_model(self, args, step):
target = self.bmanager.spc_buffer.sample(self.bsize)
target = encode_target(target)
target['seg_batch'] = target['seg_batch'].long()
output = self.model(target['obs_batch'],
target['act_batch'],
action_var=target['prev_action'])
loss = 0.0
batch_thr = self.args.thr
threshold = batch_thr * self.pstep
if self.args.use_depth:
depth_pred = output["depth_pred"].view(-1, self.img_h, self.img_w)
depth_target = target["depth_batch"].view(-1, self.img_h,
self.img_w)
depth_loss = self.depth_loss_func(depth_pred, depth_target)
loss += depth_loss
print("depth loss: {}".format(depth_loss.data.cpu().numpy()))
if self.args.use_detection:
original_bboxes = target['original_bboxes']
bboxes_nums = [[
original_bboxes[i][j].size / 5 for j in range(self.pstep + 1)
] for i in range(self.bsize)]
bboxes_ind = [
np.array(np.where(np.array(bboxes_nums[i]) > 0))
for i in range(self.bsize)
]
nonempty_batches = []
empty_batches = []
for i in range(self.bsize):
if bboxes_ind[i].size > 0 and 0 in bboxes_ind[i]:
# ensure that the first frame in the episode contains at least one vehicle GT
nonempty_batches.append(i)
else:
empty_batches.append(i)
frame_idx = []
for batch_ind in nonempty_batches:
for frame_ind in bboxes_ind[batch_ind][0]:
frame_idx.append(batch_ind * (self.pstep + 1) + frame_ind)
if len(frame_idx) < threshold:
print(
color_text(
'No enough positive samples to train detector ...',
'green'))
instance_loss = 0
else:
instance_loss = ins_loss(
step,
target,
output,
self.detect_loss_func,
self.coll_with_loss_func,
self.logger,
use_coll_with=self.args.use_colls_with)
loss += instance_loss
print("detector loss: {}".format(instance_loss))
# Loss Part #2: loss from future event happening prediction
loss += event_losses(step, target, output, get_accuracy,
self.event_loss_func, self.eventloss_weights,
self.logger)
# Loss Part #3: loss from future speed prediction
if args.use_speed:
speed_pred = output['speed']
speed_target = target['sp_batch'][:, 1:].unsqueeze(dim=2)
speedloss = one_loss(step, speed_target, speed_pred,
self.speed_loss_func, "speed", self.logger)
loss += self.speedloss_weight * speedloss
# Loss Part #3: loss from future pixelwise semantic label prediction
seg_pred = output['seg_pred'].view(-1, self.classes, self.img_h,
self.img_w)
seg_target = target['seg_batch'].view(-1, self.img_h, self.img_w)
segloss = one_loss(step, seg_target, seg_pred, self.seg_loss_func,
"seg", self.logger)
loss += self.segloss_weight * segloss
self.logger.write(step, "total_loss", loss.item())
gc.collect()
return loss
refer = link.get('href')
if refer.startswith('/'):
links.append(purl.scheme + '://' + purl.netloc + refer)
elif refer.startswith('#'):
links.append(url + refer)
else:
p = urlparse(refer)
if p.netloc and p.scheme:
links.append(refer)
links = list(set(links))
# print(links)
# exit(1)
spaces = '{: <100} {:>20} {:>40}'
print(
spaces.format(color_text('link', 'cyan'), color_text('filesize', 'cyan'),
color_text('filename', 'cyan')))
for link in links:
try:
head = session.head(link, allow_redirects=True, timeout=10).headers
except requests.ConnectionError as e:
print('There is a connection error with link', link,
'and the error is \n', str(e))
continue
if is_downloadable(head.get('content-type')):
# print(head)
filename = get_filename_from_cd(head.get('content-disposition'))
if not filename:
filename = link.split('/')[-1]
file_size = int(head['content-length'])
def print_devices_comparison(with_color=True, with_locations=False):
"""
Prints a table showing when each directory was last backed up on each
device.
"""
nominal_table_width = 70
no_columns = len(config.DEVICES) + 1
column_width = nominal_table_width / no_columns
table_width = (column_width * no_columns) + 1
horizontal_border = (('+' + ('-' * (column_width - 1))) * (no_columns)) + \
'+'
# Print the table heading row.
print '+{:-<{width}}+'.format('', width=(table_width - 2))
print '|{:^{width}}|'.format('<<< All devices >>>', width=(table_width - 2))
# Print the subheading row.
print '+{:-<{width1}}+{:-<{width2}}+'.format(
'',
'',
width1=(column_width - 1),
width2=((column_width * (no_columns - 1)) - 1)
)
print '|{:^{width1}}|{:^{width2}}|'.format(
'~ Directory ~',
'~ Approximate backup age ~',
width1=(column_width - 1),
width2=((column_width * (no_columns - 1)) - 1)
)
print horizontal_border
# Print the column headings row.
column_heading_row = '|{:^{width}}' .format('', width=(column_width - 1))
for device in config.DEVICES:
max_text_width = column_width - 1
column_heading_row += '|{:^{width}}'.format(
device['name'][:max_text_width],
width=max_text_width
)
column_heading_row += '|'
print column_heading_row
print horizontal_border
# Print each directory's row.
for directory in config.DIRECTORIES:
directory_row = '| {:<{width}}'.format(
directory['name'],
width=(column_width - 2)
)
for d in config.DEVICES:
device = Device(d)
elapsed_seconds = device.directory_age(directory)
if elapsed_seconds:
raw_msg = readable_duration(elapsed_seconds)
msg = '{:^{width}}'.format(raw_msg, width=(column_width - 2))
else:
msg = '{:^{width}}'.format(
'-',
width=(column_width - 2)
)
if with_color and elapsed_seconds > (60 * 60 * 24 * 3):
msg = color_text(msg, 'red')
elif with_color and elapsed_seconds > (60 * 60 * 24 * 1):
msg = color_text(msg, 'amber')
elif with_color and elapsed_seconds:
msg = color_text(msg, 'green')
directory_row += '| {}'.format(msg)
directory_row += '|'
print directory_row
print horizontal_border
# Print each device's location.
if with_locations:
print ''
print horizontal_border
location_row = '| {:<{width}}'.format(
'Location',
width=(column_width - 2)
)
for d in config.DEVICES:
device = Device(d)
max_text_width = column_width - 1
location_row += '|{:^{width}}'.format(
device.location[:max_text_width],
width=max_text_width
)
location_row += '|'
print location_row
print horizontal_border
# Add two blank lines at the end for visual clarity.
print'\n'
def train_policy(args, env, max_steps=40000000):
guides = generate_guide_grid(args.bin_divide)
train_net, net, optimizer, epoch, exploration, num_steps = init_models(args)
buffer_manager = BufferManager(args)
action_manager = ActionSampleManager(args, guides)
action_var = Variable(torch.from_numpy(np.array([-1.0, 0.0])).repeat(1, args.frame_history_len - 1, 1), requires_grad=False).float()
# prepare video recording
if args.recording:
video_folder = os.path.join(args.video_folder, "%d" % num_steps)
os.makedirs(video_folder, exist_ok=True)
if args.sync:
video = cv2.VideoWriter(os.path.join(video_folder, 'video.avi'),
cv2.VideoWriter_fourcc(*'MJPG'),
24.0, (args.frame_width, args.frame_height), True)
else:
video = None
signal = mp.Value('i', 1)
p = mp.Process(target=record_screen,
args=(signal,
os.path.join(video_folder, 'video.avi'),
1280, 800, 24))
p.start()
# initialize environment
obs, info = env.reset()
if args.recording:
log_frame(obs, buffer_manager.prev_act, video_folder, video)
num_episode = 1
print('Start training...')
for step in range(num_steps, max_steps):
obs_var = buffer_manager.store_frame(obs, info)
action, guide_action = action_manager.sample_action(net=net,
obs=obs,
obs_var=obs_var,
action_var=action_var,
exploration=exploration,
step=step,
explore=num_episode % 2)
obs, reward, done, info = env.step(action)
print("action [{0:.2f}, {1:.2f}]".format(action[0], action[1]) + " " +
"collision {}".format(str(bool(info['collision']))) + " " +
"off-road {}".format(str(bool(info['offroad']))) + " " +
"speed {0:.2f}".format(info['speed']) + " " +
"reward {0:.2f}".format(reward) + " " +
"explore {0:.2f}".format(exploration.value(step))
)
action_var = buffer_manager.store_effect(guide_action=guide_action,
action=action,
reward=reward,
done=done,
collision=info['collision'],
offroad=info['offroad'])
if args.recording:
log_frame(obs, action, video_folder, video)
if done:
print('Episode {} finished'.format(num_episode))
if not args.sync and args.recording:
signal.value = 0
p.join()
del p
# train SPN
if buffer_manager.spc_buffer.can_sample(args.batch_size) and ((not args.sync and done) or (args.sync and step % args.learning_freq == 0)):
# train model
for ep in range(args.num_train_steps):
optimizer.zero_grad()
loss = train_model(args=args,
net=train_net,
spc_buffer=buffer_manager.spc_buffer)
if args.use_guidance:
loss += train_guide_action(args=args,
net=train_net,
spc_buffer=buffer_manager.spc_buffer,
guides=guides)
print('loss = %0.4f\n' % loss.data.cpu().numpy())
loss.backward()
optimizer.step()
epoch += 1
net.load_state_dict(train_net.state_dict())
# save model
if epoch % args.save_freq == 0:
print(color_text('Saving models ...', 'green'))
torch.save(train_net.module.state_dict(),
os.path.join(args.save_path, 'model', 'pred_model_%09d.pt' % step))
torch.save(optimizer.state_dict(),
os.path.join(args.save_path, 'optimizer', 'optimizer.pt'))
with open(os.path.join(args.save_path, 'epoch.pkl'), 'wb') as f:
pkl.dump(epoch, f)
buffer_manager.save_spc_buffer()
print(color_text('Model saved successfully!', 'green'))
if done:
# reset video recording
if args.recording:
if args.sync:
video.release()
if sys.platform == 'linux': # save memory
os.system('ffmpeg -y -i {0} {1}'.format(
os.path.join(video_folder, 'video.avi'),
os.path.join(video_folder, 'video.mp4')
))
if os.path.exists(os.path.join(video_folder, 'video.mp4')):
os.remove(os.path.join(video_folder, 'video.avi'))
video_folder = os.path.join(args.video_folder, "%d" % step)
os.makedirs(video_folder, exist_ok=True)
video = cv2.VideoWriter(os.path.join(video_folder, 'video.avi'),
cv2.VideoWriter_fourcc(*'MJPG'),
24.0, (args.frame_width, args.frame_height), True)
else:
video_folder = os.path.join(args.video_folder, "%d" % step)
os.makedirs(video_folder, exist_ok=True)
signal.value = 1
p = mp.Process(target=record_screen,
args=(signal, os.path.join(video_folder, 'obs.avi'), 1280, 800, 24))
p.start()
num_episode += 1
obs, info = env.reset()
buffer_manager.reset(step)
action_manager.reset()
if args.recording:
log_frame(obs, buffer_manager.prev_act, video_folder, video)
def start(self):
# temp
advance_dirs = {
'Merged_vcf': '{analydir}/Advance/{newjob}/Merged_vcf',
'ACMG': '{analydir}/Advance/{newjob}/ACMG',
'FilterSV': '{analydir}/Advance/{newjob}/FilterSV',
'FilterCNV': '{analydir}/Advance/{newjob}/FilterCNV',
'Noncoding': '{analydir}/Advance/{newjob}/Noncoding',
'ModelF': '{analydir}/Advance/{newjob}/ModelF',
'Share': '{analydir}/Advance/{newjob}/Share',
'Denovo': '{analydir}/Advance/{newjob}/Denovo',
'Linkage': '{analydir}/Advance/{newjob}/Linkage',
'ROH': '{analydir}/Advance/{newjob}/ROH',
'Network': '{analydir}/Advance/{newjob}/Network',
'Pathway': '{analydir}/Advance/{newjob}/Pathway',
'PPI': '{analydir}/Advance/{newjob}/PPI',
'HLA': '{analydir}/Advance/{newjob}/HLA',
'SiteAS': '{analydir}/Advance/{newjob}/SiteAS',
'GeneAS': '{analydir}/Advance/{newjob}/GeneAS',
'IntegrateResult': '{analydir}/Advance/{newjob}/IntegrateResult',
'Disease': '{analydir}/Advance/{newjob}/Disease',
'BriefResults': '{analydir}/Advance/{newjob}/BriefResults',
}
for k, v in advance_dirs.iteritems():
self.args.update({k: v.format(**self.args)})
# print self.args['SiteAS']
# exit()
# print self.analy_array
print 'hello, {}'.format(self.username)
# Require rawdata or not
qc_status = utils.get_status('qc', self.startpoint,
config.ANALYSIS_POINTS)
mapping_status = utils.get_status('bwa_mem', self.startpoint,
config.ANALYSIS_POINTS)
print 'qc status:', qc_status
print 'mapping status:', mapping_status
ANALY_DICT = utils.get_analysis_dict(self.analy_array,
config.ANALYSIS_CODE)
self.args.update({'ANALY_DICT': ANALY_DICT})
# print ANALY_DICT.keys();exit()
softwares = utils.get_softwares(self.analy_array,
self.args['ANALY_DICT'], self.args,
self.seqstrag)
# pprint(softwares);exit()
self.args.update({'softwares': softwares})
# check inputs
self.queues = utils.check_queues(self.queues, self.username)
self.args.update({'queues': self.queues})
# use sentieon specific queues if needed
if 'sentieon' in softwares.values():
print 'add sentieon_queues'
sentieon_queues = self.queues
if config.CONFIG.has_option('resource', 'sentieon_queues'):
sentieon_queues = config.CONFIG.get(
'resource', 'sentieon_queues').split(',')
sentieon_queues = utils.check_queues(sentieon_queues,
self.username)
if not sentieon_queues:
sentieon_queues = self.queues
self.args.update({'sentieon_queues': sentieon_queues})
# print self.args['sentieon_queues'];exit()
# print sentieon_queues;exit()
utils.check_analy_array(self.seqstrag, self.analy_array,
config.ANALYSIS_CODE)
utils.check_files(self.pn, self.samp_info, self.samp_list)
newTR = utils.check_target_region(config.CONFIG, self.seqstrag,
self.refgenome, self.rawTR)
self.args.update({'TR': newTR})
print 'analysis items:'
for analysis_code in self.analy_array:
print utils.color_text(
'{:4} {}'.format(analysis_code,
config.ANALYSIS_CODE[analysis_code][0]),
'yellow')
# Analysis start point
if self.startpoint:
if self.startpoint in config.ANALYSIS_POINTS:
print 'start point: {}'.format(
utils.color_text(self.startpoint))
else:
print '[error] invalid startpoint: {}'.format(
utils.color_text(self.startpoint))
print 'maybe you want to choose: {}'.format(
utils.color_text(
process.extractOne(self.startpoint,
config.ANALYSIS_POINTS.keys())[0],
'cyan'))
print 'available startpoints are as follows:\n {}'.format(
' '.join(config.ANALYSIS_POINTS.keys()))
exit(1)
is_advance = max(self.analy_array) > 6.1
project = utils.Project(self.analydir, self.samp_info,
self.samp_info_done, self.samp_list,
self.qc_list, qc_status, mapping_status,
is_advance)
# Extract sample_info
print 'extract sample informations...'
fenqi, tissue, disease_name, sample_infos, sample_infos_all, sample_done = project.get_sample_infos(
self.samp_list, self.samp_info, self.samp_info_done, is_advance)
database = '{}/project/DisGeNet.json'.format(
config.CONFIG.get('software', 'soft_dir'))
disease_ids = utils.get_disease_id(disease_name, database)
self.args.update({
'disease_name': disease_name,
'disease_ids': disease_ids,
})
sample_infos_waiting = {
sampleid: infos
for sampleid, infos in sample_infos.iteritems()
if sampleid not in sample_done
}
self.args.update({'sample_infos_waiting': sample_infos_waiting})
# print sample_infos_waiting
# exit()
# print 'fenqi:', fenqi
# print 'tissue:', tissue
# exit()
sample_lists = project.get_sample_lists
# print sample_lists
# print sample_infos.keys()
# print sample_infos_all.keys()
# for sample in sample_infos:
# print sample, sample_infos[sample]['familyid']
# exit()
if mapping_status == 'waiting':
sample_lists = project.update_qc_list()
print ' report number: {}'.format(utils.color_text(fenqi))
if disease_name:
print ' disease name: {}'.format(utils.color_text(disease_name))
print ' disease id: {}'.format(utils.color_text(disease_ids))
if tissue:
print ' tissue: {}'.format(utils.color_text(tissue))
print ' samples ({}): {}'.format(
len(sample_infos), utils.color_text(sample_infos.keys()))
if sample_done:
print ' samples done({}): {}'.format(
len(sample_done), utils.color_text(sample_done))
# Update qc_list and extract sample_list
# print 'update qc_list...'
# print json.dumps(sample_lists, indent=2)
# set memory according seqstrag
print 'set analysis memory...'
if self.seqstrag == 'WGS':
print 'upate memory for WGS...'
for analysis, memory in config.ANALYSIS_MEM_WGS.items():
if analysis in config.ANALYSIS_POINTS:
config.ANALYSIS_POINTS[analysis][0] = memory
# exit()
# ===========================================================
# ===========================================================
print '>>> pipeline start...'
mutation_soft, sv_soft, cnv_soft, denovo_soft = [
softwares[each] for each in ('mutation', 'sv', 'cnv', 'denovo')
]
print ' mutation_soft:{}, sv_soft:{}, cnv_soft:{}, denovo_soft:{}'.format(
mutation_soft, sv_soft, cnv_soft, denovo_soft)
# QC
if ANALY_DICT['quality_control'] and qc_status == 'waiting':
utils.print_color('> QC', 'white')
QC(self.args, self.jobs, self.orders, sample_lists, config).start()
# Mapping
if ANALY_DICT['mapping']:
utils.print_color('> Mapping', 'white')
Mapping(self.args, self.jobs, self.orders, sample_lists,
sample_infos, config, qc_status, mapping_status).start()
# Mutation
if ANALY_DICT['snpindel_call']:
utils.print_color('> Mutation', 'white')
Mutation(self.args, self.jobs, self.orders, sample_lists,
sample_infos, config).start()
# SV
if ANALY_DICT['sv_call']:
utils.print_color('> SV', 'white')
SV(self.args, self.jobs, self.orders, sample_infos, config).start()
# CNV
if ANALY_DICT['cnv_call']:
utils.print_color('> CNV', 'white')
CNV(self.args, self.jobs, self.orders, sample_infos,
config).start()
# FilterDB
if ANALY_DICT['filter']:
utils.print_color('> FilterDB', 'white')
FilterDB(self.args, self.jobs, self.orders, mutation_soft, sv_soft,
cnv_soft, sample_infos, config, disease_name, tissue,
ANALY_DICT).start()
# ModelF
if ANALY_DICT['filter_model']:
utils.print_color('> Model', 'white')
FilterModel(self.args, self.jobs, self.orders, mutation_soft,
sv_soft, cnv_soft, sample_infos, config).start()
# Denovo
if ANALY_DICT['denovo']:
utils.print_color('> Denovo', 'white')
Denovo(self.args, self.jobs, self.orders, mutation_soft, sv_soft,
cnv_soft, denovo_soft, sample_infos, config,
ANALY_DICT).start()
# Linkage
if ANALY_DICT['linkage']:
utils.print_color('> Linkage', 'white')
Linkage(self.args, self.jobs, self.orders, mutation_soft, sv_soft,
cnv_soft, denovo_soft, sample_infos_all, config,
ANALY_DICT).start()
# IntegrateResult
if any(ANALY_DICT[analysis] for analysis in
['filter', 'filter_model', 'denovo', 'phenolyzer']):
utils.print_color('> IntegrateResult', 'white')
IntegrateResult(self.args, self.jobs, self.orders, config).start()
# ROH
if ANALY_DICT['roh']:
utils.print_color('> ROH', 'white')
ROH(self.args, self.jobs, self.orders, sample_infos, mutation_soft,
config).start()
# OTHER
other = Other(self.args, self.jobs, self.orders, config, disease_name)
# IBD
if any(ANALY_DICT[each]
for each in ['filter_model', 'linkage', 'denovo'
]) and len(sample_infos_waiting) > 1:
utils.print_color('> IBD', 'white')
other.ibd()
# Network
if ANALY_DICT['phenolyzer']:
utils.print_color('> Phenolyzer', 'white')
other.phenolyzer()
# Pathway
if ANALY_DICT['pathway']:
utils.print_color('> Pathway', 'white')
other.pathway()
# PPI
if ANALY_DICT['ppi']:
utils.print_color('> PPI', 'white')
other.ppi()
# SiteAS
if ANALY_DICT['site_association']:
utils.print_color('> SiteAS', 'white')
Association(self.args, self.jobs, self.orders,
config).site_association()
# GeneAS
if ANALY_DICT['gene_association']:
utils.print_color('> GeneAS', 'white')
Association(self.args, self.jobs, self.orders,
config).gene_association()
# HLA
if ANALY_DICT['hla']:
utils.print_color('> HLA', 'white')
HLA(self.args, self.jobs, self.orders, sample_lists, sample_infos,
config, qc_status).start()
# result and report
utils.print_color('> Result', 'white')
Result(self.args, self.jobs, self.orders, config).start()
utils.print_color('> Report', 'white')
Report(self.args, self.jobs, self.orders, config).start()
# job summary
print 'lenght of jobs waiting/total: {}/{}'.format(
len([job for job in self.jobs if job.get('status') == 'waiting']),
len(self.jobs))
utils.write_job(self.analydir, self.newjob, self.jobs, self.orders)
print '{:-^80}'.format(' all done ')