def poll_events():
event_list = []
for h in handlers:
event_list.extend(h.controller.log)
h.controller.log = []
ship_output = {}
bullet_output = {}
for e in event_list:
if e[0] == 'ship':
if not ship_output.has_key('normal'):
ship_output['normal'] = []
ship_output['normal'].append((Serialize.serializeShip(e[1]), e[2], e[3], e[4], e[5]))
elif e[0] == 'bullet':
if not bullet_output.has_key('normal'):
bullet_output['normal'] = []
bullet_output['normal'].append((Serialize.serializeBullet(e[1]), e[2]))
for e in event_log.ship_deaths:
if not ship_output.has_key('death'):
ship_output['death'] = []
ship_output['death'].append((Serialize.serializeShip(e[0]), e[1], False, False, False))
event_log.ship_deaths = []
for e in event_log.ship_reflects:
if not ship_output.has_key('reflect'):
ship_output['reflect'] = []
ship_output['reflect'].append((Serialize.serializeShip(e[0]), e[2]))
ship_output['reflect'].append((Serialize.serializeShip(e[1]), e[2]))
event_log.ship_reflects = []
for e in event_log.wall_reflects:
if not ship_output.has_key('reflect'):
ship_output['reflect'] = []
ship_output['reflect'].append((Serialize.serializeShip(e[0]), e[2]))
event_log.wall_reflects = []
for e in event_log.bullet_deaths:
if not bullet_output.has_key('death'):
bullet_output['death'] = []
bullet_output['death'].append((Serialize.serializeBullet(e[0]), Serialize.serializeRect(e[1]), e[2]))
event_log.bullet_deaths = []
for e in event_log.bullet_timeouts:
if not bullet_output.has_key('timeout'):
bullet_output['timeout'] = []
bullet_output['timeout'].append((Serialize.serializeBullet(e[0]), e[1]))
event_log.bullet_timeouts = []
full_output = {}
if len(ship_output)>0:
full_output['ship'] = ship_output
if len(bullet_output)>0:
full_output['bullet'] = bullet_output
if len(full_output)>0:
msg = { 'update' : full_output }
for h in handlers:
h.do_send(msg)
def save(self):
""" Save information about library in text file.
Args:
filename(str): Set name of the file which is used to upload
information about library.
"""
specifier = "wb" if self.serialization_type == srz.pickle_type else "w"
with open(self.filename, specifier) as target_file:
srz.save([self.__users_list, self.__books_list], target_file,
self.serialization_type)
last_session_data_save(self.serialization_type)
def on_open(self):
# Grouped together to handle multiple players (new connection)
player_ship = Ship((320, 240), (15, 15), SHOOT_DELAY, SPEED,
VELOCITY_CAP, ANGULAR_VELOCITY,
random_respawn(min_respawn, max_respawn))
logic.ship_list.append(player_ship)
self.controller = ServerSideController(player_ship, logic, BULLET_SIZE,
BULLET_SPEED, BULLET_DURATION,
SHOOT_DELAY, SHIELD_SIZE)
logic.onLogicUpdate += self.controller.update
self.do_send({
'start': {
'walls':
[Serialize.serializeRect(wall) for wall in logic.wall_list],
'ticks':
TICKS,
'speed':
SPEED,
'bspeed':
BULLET_SPEED,
'maxvelo':
VELOCITY_CAP,
'angular':
ANGULAR_VELOCITY,
'current':
logic.current_tick,
'id':
player_ship.id
}
})
#logic.onLogicUpdate+=self.onLogicUpdate
handlers.append(self)
def fit_p():
read_positions_fn = '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-1/results/mRNA-rich-1_read_positions.txt'
#read_positions_fn = '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-2/results/mRNA-rich-2_read_positions.txt'
#read_positions_fn = '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_ori/results/RH_ori_read_positions.txt'
genes = Serialize.read_file(read_positions_fn, 'read_positions')
min_length = 5000
p_lsq = leastsq(residuals, 7.8e-5, args=(genes, min_length), full_output=True)
print p_lsq
return p_lsq
def total_counts_given_p():
mRNA_experiments = [
('Ingolia_mRNA_1', '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-1/results/mRNA-rich-1_read_positions.txt'),
#('Ingolia_mRNA_2', '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-2/results/mRNA-rich-2_read_positions.txt'),
#('Nagalakshmi_RH_ori', '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_ori/results/RH_ori_read_positions.txt'),
#('Nagalakshmi_RH_bio', '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_bio/results/RH_bio_read_positions.txt'),
#('Nagalakshmi_dT_ori', '/home/jah/projects/arlen/experiments/nagalakshmi_science/dT_ori/results/dT_ori_read_positions.txt'),
#('Nagalakshmi_dT_bio', '/home/jah/projects/arlen/experiments/nagalakshmi_science/dT_bio/results/dT_bio_read_positions.txt'),
]
experiments = [(name, counts_from_genes(Serialize.read_file(fn, 'read_positions')))
for name, fn in mRNA_experiments]
min_length = 0000
max_length = 10000
plot_to = 2000
fig_cumulative, ax_cumulative = plt.subplots()
xs = np.arange(0, -plot_to, -1)
for name, counts_generator in experiments:
print name
total_uniform_counts = np.zeros(100000)
total_geometric_counts = np.zeros(100000)
total_actual_counts = np.zeros(100000)
for counts in counts_generator:
l_g = len(counts)
if not (min_length < l_g < max_length):
continue
r_g = counts.sum()
uniform_counts = np.ones(l_g) / l_g * r_g
# Some weirdness about whether to include 0 or not in make_P_distribution
#geometric_counts = make_P_distribution(l_g, 4e-4)[1:] * r_g
geometric_counts = make_P_distribution(l_g, 7.8e-5)[1:] * r_g
#geometric_counts = make_P_distribution(l_g, 4.6e-5)[1:] * r_g
counts = counts[::-1]
total_actual_counts[:l_g] += counts
total_uniform_counts[:l_g] += uniform_counts
total_geometric_counts[:l_g] += geometric_counts
print total_actual_counts.sum()
print total_uniform_counts.sum()
print total_geometric_counts.sum()
ax_cumulative.plot(xs, smoothed(total_actual_counts[:plot_to], 5), '-', label=name + '_actual_smoothed')
ax_cumulative.plot(xs, total_uniform_counts[:plot_to], '-', linewidth=2, label=name + '_uniform')
ax_cumulative.plot(xs, total_geometric_counts[:plot_to], '-', linewidth=2, label=name + '_geometric')
ax_cumulative.legend()
xlabel = 'Position relative to end'
ax_cumulative.set_xlabel(xlabel)
ax_cumulative.set_ylabel('Mapped read counts')
def counts_from_read_positions_fn(read_positions_fn, from_end):
gene_infos = Serialize.read_file(read_positions_fn, 'read_positions')
for gene_name in gene_infos:
#if gene_name == 'YLR256W':
# continue
if from_end:
counts = gene_infos[gene_name]['all'].relative_to_end
else:
counts = gene_infos[gene_name]['all']
yield gene_name, counts
def counts_from_read_positions_fn(read_positions_fn, from_end):
gene_infos = Serialize.read_file(read_positions_fn, 'read_positions')
for gene_name in gene_infos:
#if gene_name == 'YLR256W':
# continue
if from_end:
counts = gene_infos[gene_name]['all'].relative_to_end
else:
counts = gene_infos[gene_name]['all']
yield gene_name, counts
def fit_p():
read_positions_fn = '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-1/results/mRNA-rich-1_read_positions.txt'
#read_positions_fn = '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-2/results/mRNA-rich-2_read_positions.txt'
#read_positions_fn = '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_ori/results/RH_ori_read_positions.txt'
genes = Serialize.read_file(read_positions_fn, 'read_positions')
min_length = 5000
p_lsq = leastsq(residuals,
7.8e-5,
args=(genes, min_length),
full_output=True)
print p_lsq
return p_lsq
def on_open(self):
# Grouped together to handle multiple players (new connection)
player_ship = Ship((320, 240), (15, 15), SHOOT_DELAY, SPEED, VELOCITY_CAP, ANGULAR_VELOCITY, random_respawn(min_respawn, max_respawn))
logic.ship_list.append(player_ship)
self.controller = ServerSideController(player_ship, logic, BULLET_SIZE, BULLET_SPEED, BULLET_DURATION, SHOOT_DELAY, SHIELD_SIZE)
logic.onLogicUpdate+=self.controller.update
self.do_send({'start': { 'walls': [Serialize.serializeRect(wall) for wall in logic.wall_list],
'ticks': TICKS,
'speed' : SPEED,
'bspeed' : BULLET_SPEED,
'maxvelo' : VELOCITY_CAP,
'angular' : ANGULAR_VELOCITY,
'current' : logic.current_tick,
'id' : player_ship.id}})
#logic.onLogicUpdate+=self.onLogicUpdate
handlers.append(self)
def load(self):
""" Load information about library users and books
Args:
filename(str): Set name of the file which is used to upload
information about library.
"""
load_type = last_session_save_type()
specifier = "rb" if load_type == srz.pickle_type else "r"
try:
with open(self.filename, specifier) as source:
self.__users_list, self.__books_list = srz.load(
source, load_type)
except OSError:
self.__users_list = []
self.__books_list = []
def work():
modellist = []
for item in Serialize.Reader().deserialized:
model = Model.Model(item)
modellist.append(model)
return modellist
def poll_events():
event_list = []
for h in handlers:
event_list.extend(h.controller.log)
h.controller.log = []
ship_output = {}
bullet_output = {}
for e in event_list:
if e[0] == 'ship':
if not ship_output.has_key('normal'):
ship_output['normal'] = []
ship_output['normal'].append(
(Serialize.serializeShip(e[1]), e[2], e[3], e[4], e[5]))
elif e[0] == 'bullet':
if not bullet_output.has_key('normal'):
bullet_output['normal'] = []
bullet_output['normal'].append(
(Serialize.serializeBullet(e[1]), e[2]))
for e in event_log.ship_deaths:
if not ship_output.has_key('death'):
ship_output['death'] = []
ship_output['death'].append(
(Serialize.serializeShip(e[0]), e[1], False, False, False))
event_log.ship_deaths = []
for e in event_log.ship_reflects:
if not ship_output.has_key('reflect'):
ship_output['reflect'] = []
ship_output['reflect'].append((Serialize.serializeShip(e[0]), e[2]))
ship_output['reflect'].append((Serialize.serializeShip(e[1]), e[2]))
event_log.ship_reflects = []
for e in event_log.wall_reflects:
if not ship_output.has_key('reflect'):
ship_output['reflect'] = []
ship_output['reflect'].append((Serialize.serializeShip(e[0]), e[2]))
event_log.wall_reflects = []
for e in event_log.bullet_deaths:
if not bullet_output.has_key('death'):
bullet_output['death'] = []
bullet_output['death'].append((Serialize.serializeBullet(e[0]),
Serialize.serializeRect(e[1]), e[2]))
event_log.bullet_deaths = []
for e in event_log.bullet_timeouts:
if not bullet_output.has_key('timeout'):
bullet_output['timeout'] = []
bullet_output['timeout'].append(
(Serialize.serializeBullet(e[0]), e[1]))
event_log.bullet_timeouts = []
full_output = {}
if len(ship_output) > 0:
full_output['ship'] = ship_output
if len(bullet_output) > 0:
full_output['bullet'] = bullet_output
if len(full_output) > 0:
msg = {'update': full_output}
for h in handlers:
h.do_send(msg)
def HTTP_request():
global option, threads_list, max_threads, delay, os, dt
threads_list = []
requests = file_string.split('<item>')
requests.pop(0)
payloadstype = option
PayloadGenerator.setType(option)
payloadslist = PayloadGenerator.payloadslist(option)
for request in requests:
path = find_between(request, '<url><![CDATA[', ']]></url>')
raw_request = find_between(request, '"false"><![CDATA[', ']]></request>')
raw_header, data = raw_request.split('\r\n\r\n', 1)
lines = raw_header.split('\r\n')
method = ''
if 'POST' in lines[0]:
method = 'POST'
else:
if 'GET' in lines[0]:
method = 'GET'
headers = {}
i = 1
while i < len(lines):
info = lines[i].split(': ', 1)
if 'Content-Length' not in info[0]:
headers.update({info[0]: info[1]})
i = i + 1
try:
if method == 'POST':
original_request = post_call(path, data, headers)
if 'multipart/form-data' in headers.get('Content-Type'):
boundaries = data.split('\n\n')
if payloadstype == 'pp':
ParameterPollution.multi_post_call(path, headers, payloadslist, boundaries, original_request)
if payloadstype == 'si':
SOAPInjection.multi_post_call(path, headers, payloadslist, boundaries, original_request)
if payloadstype == 'ti':
TemplateInjection.multi_post_call(path, headers, payloadslist, boundaries, original_request)
if payloadstype == 'sr':
Serialize.multi_post_call(path, headers, payloadslist, boundaries, original_request)
if payloadstype == 'op':
OraclePadding.multi_post_call(path, headers, payloadslist, boundaries, original_request)
if payloadstype == 'xxe':
XXE.multi_post_call(path, headers, payloadslist, boundaries, original_request)
else:
post_params = data.split('&')
if payloadstype == 'pp':
ParameterPollution.common_post_call(path, headers, payloadslist, post_params, original_request)
if payloadstype == 'si':
SOAPInjection.common_post_call(path, headers, payloadslist, post_params, original_request)
if payloadstype == 'ti':
TemplateInjection.common_post_call(path, headers, payloadslist, post_params, original_request)
if payloadstype == 'sr':
Serialize.common_post_call(path, headers, payloadslist, post_params, original_request)
if payloadstype == 'op':
OraclePadding.common_post_call(path, headers, payloadslist, post_params, original_request)
if payloadstype == 'xxe':
XXE.common_post_call(path, headers, payloadslist, post_params, original_request)
if method == 'GET':
if '?' in path:
original_request = get_call(path, headers)
if payloadstype == 'pp':
ParameterPollution.get_call(path, headers, data, payloadslist, original_request)
if payloadstype == 'si':
SOAPInjection.get_call(path, headers, data, payloadslist, original_request)
if payloadstype == 'ti':
TemplateInjection.get_call(path, headers, data, payloadslist, original_request)
if payloadstype == 'sr':
Serialize.get_call(path, headers, data, payloadslist, original_request)
if payloadstype == 'op':
OraclePadding.get_call(path, headers, data, payloadslist, original_request)
if payloadstype == 'xxe':
XXE.get_call(path, headers, data, payloadslist, original_request)
else:
#no params to test
pass
except urllib2.HTTPError as err:
print err
def total_counts_given_p():
mRNA_experiments = [
('Ingolia_mRNA_1',
'/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-1/results/mRNA-rich-1_read_positions.txt'
),
#('Ingolia_mRNA_2', '/home/jah/projects/arlen/experiments/ingolia_science/mRNA-rich-2/results/mRNA-rich-2_read_positions.txt'),
#('Nagalakshmi_RH_ori', '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_ori/results/RH_ori_read_positions.txt'),
#('Nagalakshmi_RH_bio', '/home/jah/projects/arlen/experiments/nagalakshmi_science/RH_bio/results/RH_bio_read_positions.txt'),
#('Nagalakshmi_dT_ori', '/home/jah/projects/arlen/experiments/nagalakshmi_science/dT_ori/results/dT_ori_read_positions.txt'),
#('Nagalakshmi_dT_bio', '/home/jah/projects/arlen/experiments/nagalakshmi_science/dT_bio/results/dT_bio_read_positions.txt'),
]
experiments = [
(name, counts_from_genes(Serialize.read_file(fn, 'read_positions')))
for name, fn in mRNA_experiments
]
min_length = 0000
max_length = 10000
plot_to = 2000
fig_cumulative, ax_cumulative = plt.subplots()
xs = np.arange(0, -plot_to, -1)
for name, counts_generator in experiments:
print name
total_uniform_counts = np.zeros(100000)
total_geometric_counts = np.zeros(100000)
total_actual_counts = np.zeros(100000)
for counts in counts_generator:
l_g = len(counts)
if not (min_length < l_g < max_length):
continue
r_g = counts.sum()
uniform_counts = np.ones(l_g) / l_g * r_g
# Some weirdness about whether to include 0 or not in make_P_distribution
#geometric_counts = make_P_distribution(l_g, 4e-4)[1:] * r_g
geometric_counts = make_P_distribution(l_g, 7.8e-5)[1:] * r_g
#geometric_counts = make_P_distribution(l_g, 4.6e-5)[1:] * r_g
counts = counts[::-1]
total_actual_counts[:l_g] += counts
total_uniform_counts[:l_g] += uniform_counts
total_geometric_counts[:l_g] += geometric_counts
print total_actual_counts.sum()
print total_uniform_counts.sum()
print total_geometric_counts.sum()
ax_cumulative.plot(xs,
smoothed(total_actual_counts[:plot_to], 5),
'-',
label=name + '_actual_smoothed')
ax_cumulative.plot(xs,
total_uniform_counts[:plot_to],
'-',
linewidth=2,
label=name + '_uniform')
ax_cumulative.plot(xs,
total_geometric_counts[:plot_to],
'-',
linewidth=2,
label=name + '_geometric')
ax_cumulative.legend()
xlabel = 'Position relative to end'
ax_cumulative.set_xlabel(xlabel)
ax_cumulative.set_ylabel('Mapped read counts')
def on_msg(self, msg):
if 'start' in msg:
global SERVER_TICKS, SPEED, BULLET_SPEED, VELOCITY_CAP, ANGULAR_VELOCITY, current
SERVER_TICKS = msg['start']['ticks']
SPEED = msg['start']['speed']
BULLET_SPEED = msg['start']['bspeed']
VELOCITY_CAP = msg['start']['maxvelo']
ANGULAR_VELOCITY = msg['start']['angular']
server_current = current = msg['start']['current']
self.ship_id = msg['start']['id']
for wall in msg['start']['walls']:
self.view.wall_list.append(Serialize.deserializeRect(wall))
elif 'update' in msg:
msginput = msg['update']
if 'ship' in msginput:
if 'normal' in msginput['ship']:
for n in msginput['ship']['normal']:
ship = Serialize.deserializeShip(n[0])
isMoving = n[2]
isLefting = n[3]
isRighting = n[4]
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
flags_dict[ship.id] = (isMoving, isLefting, isRighting)
if 'death' in msginput['ship']:
for n in msginput['ship']['death']:
ship = Serialize.deserializeShip(n[0])
isMoving = n[2]
isLefting = n[3]
isRighting = n[4]
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
flags_dict[ship.id] = (isMoving, isLefting, isRighting)
self.controller.onShipDeath.fire(ship)
if 'reflect' in msginput['ship']:
for n in msginput['ship']['reflect']:
ship = Serialize.deserializeShip(n[0])
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
if 'bullet' in msginput:
if 'normal' in msginput['bullet']:
for n in msginput['bullet']['normal']:
bullet = Serialize.deserializeBullet(n[0])
if bullet.id in bullet_dict:
found_bullet = bullet_dict[bullet.id]
found_bullet.__dict__ = bullet.__dict__.copy()
else:
bullet_dict[bullet.id] = bullet
self.view.bullet_list.append(bullet)
if 'death' in msginput['bullet']:
for n in msginput['bullet']['death']:
bullet = Serialize.deserializeBullet(n[0])
wall = Serialize.deserializeRect(n[1])
self.controller.onBulletDeath.fire(bullet, wall)
if 'timeout' in msginput['bullet']:
for n in msginput['bullet']['timeout']:
bullet = Serialize.deserializeBullet(n[0])
if bullet.id in bullet_dict:
self.view.bullet_list.remove(
bullet_dict[bullet.id])
del bullet_dict[bullet.id]
def test_json(self):
""" test for serialization with json """
output = json.dumps(self.data, default=jns.js_default)
self.output = StringIO(output)
users, books = srz.load(self.output, 'json')
self.assertEqual(self.data, [users, books])
def on_msg(self, msg):
if 'start' in msg:
global SERVER_TICKS, SPEED, BULLET_SPEED, VELOCITY_CAP, ANGULAR_VELOCITY, current
SERVER_TICKS = msg['start']['ticks']
SPEED = msg['start']['speed']
BULLET_SPEED = msg['start']['bspeed']
VELOCITY_CAP = msg['start']['maxvelo']
ANGULAR_VELOCITY = msg['start']['angular']
server_current = current = msg['start']['current']
self.ship_id = msg['start']['id']
for wall in msg['start']['walls']:
self.view.wall_list.append(Serialize.deserializeRect(wall))
elif 'update' in msg:
msginput = msg['update']
if 'ship' in msginput:
if 'normal' in msginput['ship']:
for n in msginput['ship']['normal']:
ship = Serialize.deserializeShip(n[0])
isMoving = n[2]
isLefting = n[3]
isRighting = n[4]
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
flags_dict[ship.id] = (isMoving, isLefting, isRighting)
if 'death' in msginput['ship']:
for n in msginput['ship']['death']:
ship = Serialize.deserializeShip(n[0])
isMoving = n[2]
isLefting = n[3]
isRighting = n[4]
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
flags_dict[ship.id] = (isMoving, isLefting, isRighting)
self.controller.onShipDeath.fire(ship)
if 'reflect' in msginput['ship']:
for n in msginput['ship']['reflect']:
ship = Serialize.deserializeShip(n[0])
if ship.id in ship_dict:
found_ship = ship_dict[ship.id]
found_ship.__dict__ = ship.__dict__.copy()
else:
ship_dict[ship.id] = ship
self.view.ship_list.append(ship)
if 'bullet' in msginput:
if 'normal' in msginput['bullet']:
for n in msginput['bullet']['normal']:
bullet = Serialize.deserializeBullet(n[0])
if bullet.id in bullet_dict:
found_bullet = bullet_dict[bullet.id]
found_bullet.__dict__ = bullet.__dict__.copy()
else:
bullet_dict[bullet.id] = bullet
self.view.bullet_list.append(bullet)
if 'death' in msginput['bullet']:
for n in msginput['bullet']['death']:
bullet = Serialize.deserializeBullet(n[0])
wall = Serialize.deserializeRect(n[1])
self.controller.onBulletDeath.fire(bullet, wall)
if 'timeout' in msginput['bullet']:
for n in msginput['bullet']['timeout']:
bullet = Serialize.deserializeBullet(n[0])
if bullet.id in bullet_dict:
self.view.bullet_list.remove(bullet_dict[bullet.id])
del bullet_dict[bullet.id]
