def __get_neighbours_in_P(self, pos, input_data):
"""
Returns all neighbours
to which you can go from a matrix
cell.
Args:
pos: the position from which you want get all neighbours
input_data: the input for which you create the traceback
Returns:
neighbours of the cell at position pos
"""
neighbours = []
start = AlignmentOutputData.table_vertical_gaps[pos.y][pos.x]
if pos.y >= 0:
matrix_p = AlignmentOutputData.table_vertical_gaps[pos.y - 1][pos.x]
matrix_d = AlignmentOutputData.table_values[pos.y - 1][pos.x]
up_in_p = start == matrix_p + input_data.gap_beta
up_in_d = start == matrix_d + input_data.gap_opening
if up_in_p:
neighbours.append(Vector(pos.x, pos.y - 1).create(self.MATRIX_LBL_VERTICAL_GAPS))
if up_in_d:
neighbours.append(Vector(pos.x, pos.y - 1).create(self.MATRIX_LBL_MAIN))
return neighbours
def __get_neighbours_in_Q(self, pos, input_data):
"""
Returns all neighbours
to which you can go from a matrix
cell.
Args:
pos: the position from which you want get all neighbours
input_data: the input for which you create the traceback
Returns:
neighbours of the cell at position pos
"""
neighbours = []
start = AlignmentOutputData.table_horizontal_gaps[pos.y][pos.x]
if pos.y >= 0:
matrix_q = AlignmentOutputData.table_horizontal_gaps[pos.y][pos.x - 1]
matrix_d = AlignmentOutputData.table_values[pos.y][pos.x - 1]
left_in_q = start == matrix_q + input_data.gap_beta
left_in_d = start == matrix_d + input_data.gap_opening
if left_in_q:
neighbours.append(Vector(pos.x - 1, pos.y).create(self.MATRIX_LBL_HORIZONTAL_GAPS))
if left_in_d:
neighbours.append(Vector(pos.x - 1, pos.y).create(self.MATRIX_LBL_MAIN))
return neighbours
def _get_neighbours(self, pos, input_data):
"""
Returns all neighbours
to which you can go from a matrix
cell.
Args:
pos: the position from which you want get all neighbours
input_data: the input for which you create the traceback
Returns:
neighbours of the cell at position pos
"""
neighbours = []
start = AlignmentOutputData.table_values[pos.y][pos.x]
diagonal = float(strings.NAN)
up = float(strings.NAN)
left = float(strings.NAN)
cur_char_seq_1 = strings.EMPTY
cur_char_seq_2 = strings.EMPTY
if pos.y - 1 >= 0 and pos.x - 1 >= 0:
diagonal = AlignmentOutputData.table_values[pos.y - 1][pos.x - 1]
if pos.y - 1 >= 0:
up = AlignmentOutputData.table_values[pos.y - 1][pos.x]
if pos.x - 1 >= 0:
left = AlignmentOutputData.table_values[pos.y][pos.x - 1]
if pos.y - 1 >= 0:
cur_char_seq_1 = input_data.sequence_a[pos.y - 1]
if pos.x - 1 >= 0:
cur_char_seq_2 = input_data.sequence_b[pos.x - 1]
matching = start == diagonal + input_data.cost_function.get_value(
cur_char_seq_1, cur_char_seq_2)
deletion = start == up + input_data.gap_cost
insertion = start == left + input_data.gap_cost
if matching:
neighbours.append(Vector(pos.x - 1, pos.y - 1))
if insertion:
neighbours.append(Vector(pos.x - 1, pos.y))
if deletion:
neighbours.append(Vector(pos.x, pos.y - 1))
return neighbours
def traceback_one(self, path, input_data):
"""
Returns one traceback for a given input.
It is based on the pseudo-code of Prof. Dr. Backofen
http://www.bioinf.uni-freiburg.de//Lehre/Courses/2013_SS/V_RNA/slides/nussinov.pdf (slide 13)
The code is just reversing the Nussinov recursion function.
Args:
path: list in which you store the traceback
input_data: the input for which you create the traceback
"""
current = path[-1]
if current.x <= current.y+1: # case 1: j<=i -> checking if already at inner diagonal or further
return
elif Output.table_values[current.y][current.x] == Output.table_values[current.y][current.x-1]: # case 2
path.append(Vector(current.x - 1, current.y)) # going one step to the left
self.traceback_one(path, input_data)
return
else: # case 3: checks for complementary bases on the left
current_base = input_data.sequence[current.x-1] # -1 because width of table is: len(sequence) + 1
# for all k: i<=k<j
for k in range(current.y, current.x-1-input_data.loop_length):
base = input_data.sequence[k]
# S_k and S_j complementary
if pairs.complementary(base, current_base):
current_value = Output.table_values[current.y][current.x]
value_sum = Output.table_values[current.y][k] + Output.table_values[k+1][current.x-1] + 1
# if N_{i,j} = N_{i,k-1} + N_{k+1,j-1} + 1
if current_value == value_sum:
self.base_pairs.append((k+1, current.x))
# create vectors for new positions in the matrix from which to start
left = Vector(k, current.y)
bottom = Vector(current.x-1, k+1)
left_path = copy.copy(path)
bottom_path = copy.copy(path)
left_path.append(left)
bottom_path.append(bottom)
# jump to new positions
self.traceback_one(left_path, input_data)
self.traceback_one(bottom_path, input_data)
return
def get_data(self, cost_function, gap_cost, sequence_a, sequence_b):
"""
Returns relevant data needed for example for the Feng-Doolittle algorithm.
Args:
cost_function: initialized evaluation function used to evaluate alignment
gap_cost: costs for a gap
sequence_a: first sequence
sequence_b: second sequence
Returns:
a tuple with the alignment score, the number of gaps and the length of the alignment
"""
self.__set_parameters(cost_function, gap_cost, sequence_a, sequence_b)
self.__initialize_global()
self._compute_alignments()
backtracking = Backtracking()
paths = self._traceback(
Vector(self._tbl_len_x - 1, self._tbl_len_y - 1), False,
backtracking)
gaps = self._count_gaps(paths[0])
return (AlignmentOutputData.table_values[self._tbl_len_y -
1][self._tbl_len_x - 1], gaps,
len(paths[0]) - 1)
def get_right_axis(self):
self.update_axis()
if self.right_axis is not None:
right = Vector(self.right_axis[0], self.right_axis[1])
return right
else:
raise pygame.error("right axis is 'None'")
def get_left_axis(self):
self.update_axis()
if self.left_axis is not None:
left = Vector(self.left_axis[0], self.left_axis[1])
return left
else:
raise pygame.error("left axis is 'None'")
def __init__(self, sprite_name, pos=None, sprite_group=None):
BaseSprite.__init__(self, sprite_name, sprite_group)
OBJECT_MANAGER.instance.add(self)
if pos is not None:
self.rect.centerx = pos[0]
self.rect.centery = pos[1]
self.pos = Vector(pos[0], pos[1])
def run(self, seq1_fasta_fn, seq2_fasta_fn, subst_matrix_fn, cost_gap_open,
complete_traceback):
"""
Calculate optimal alignment(s) with Needleman-Wunsch algorithm and returns outputs of this algorithm
for testing purposes.
Args:
seq1_fasta_fn: path to fasta file containing first sequence
seq2_fasta_fn: path to fasta file containing second sequence
subst_matrix_fn: path to substitution matrix
cost_gap_open: cost to open a gap
complete_traceback: If True, return all optimal alignments. Otherwise choose a random alignment.
Returns:
tuple of
(id_seq1: fasta id of first sequence,
seq1: first sequence,
id_seq2: fasta id of second sequence,
seq2: second sequence,
score: score of optimal alignment,
[(aln_string_seq1, aln_string_seq2), ...]: list of tuples containing optimal alignments)
"""
self.__evaluate_parameters(seq1_fasta_fn, seq2_fasta_fn,
subst_matrix_fn, cost_gap_open,
complete_traceback)
self.__initialize_global()
self._compute_alignments()
backtracking = Backtracking()
if self._traceback_mode == self.TRACEBACK_ALL:
AlignmentOutputData.paths = self._traceback(
Vector(self._tbl_len_x - 1, self._tbl_len_y - 1), True,
backtracking)
self._create_alignments()
else:
AlignmentOutputData.paths = self._traceback(
Vector(self._tbl_len_x - 1, self._tbl_len_y - 1), False,
backtracking)
self._create_alignments()
self._output()
return (self._data.ids[0], self._data.sequence_a, self._data.ids[1],
self._data.sequence_b,
AlignmentOutputData.table_values[self._tbl_len_y -
1][self._tbl_len_x - 1],
AlignmentOutputData.alignments)
def __init__(self, name, rows, cols, pos, sprite_group):
BaseAnimatedSprite.__init__(self,
name=name,
rows=rows,
cols=cols,
colorkey=-1,
sprite_group=sprite_group)
OBJECT_MANAGER.instance.add(self)
self.pos = Vector(pos[0], pos[1])
self.rect.center = pos
def __init__(self, angle, pos):
BaseObject.__init__(self, "pink_bullet.png", pos,
SPRITE_MANAGER.instance)
rads = radians(angle)
self.direction = Vector(sin(rads), cos(rads)).normal()
self.delete = False
BULLET_MANAGER.instance.add(self)
self.speed = 30
self.collided = False
self._rotate(angle)
def __init__(self, sprite_name, controller, pos):
BaseAnimatedObject.__init__(
self, name=sprite_name, rows=9, cols=1, pos=pos,
sprite_group=SPRITE_MANAGER.instance)
# old image is used for quicker "rotations" of images, also stops the image from
# being distorted when multiple images are rotated over and over agian.
self.old_image = self.image
self.joystick = controller
# in degrees, 0 is top, 90 is left, 180 is down, 270 is right
self.facing_direction = 0
self.moving_direction = 0
self.bullet_count = 0
self._rotate(self.facing_direction)
self.radius = self.rect.centerx - self.rect.x
self.begun_movement = False
self.play_thrust = False
# current trail could also be kicked out to trail manager, I think...
self.current_trail = Trail(color1=(0, 255, 230), color2=(255, 0, 230), color3=(0, 255, 0))
self.trails = Trail_Manager()
self.velocity = Vector(0, 0)
self.acceleration = Vector(0, 0)
self.impulse = False
self.land = False
# this isn't the proper place for cycle logic. Should kick this out somehow.
self.can_cycle = -1
# ship properties..
self.mass = MASS
self.thrust = THRUST
self.engine_thrust = Vector(0, 0)
self.first_pass = True
self.camera_center = CameraCenter("Bullet.png", self)
def calc_new_position(self, cur_pos):
if self.impulse:
self._resolve_direction_vector()
else:
self.engine_thrust.x, self.engine_thrust.y = 0, 0
# calculate acceleration.x
drag_force = Vector(
-DRAG_COEFFICIENT * self.velocity.x, -DRAG_COEFFICIENT * self.velocity.y)
self.acceleration.x = (self.engine_thrust.x + drag_force.x)/self.mass
self.acceleration.y = (self.engine_thrust.y + drag_force.y)/self.mass
self.velocity.x = self.velocity.x + (self.acceleration.x * CLOCK.get_elasped())
self.velocity.y = self.velocity.y + (self.acceleration.y * CLOCK.get_elasped()) # might have to subtract this value..
dx = (0.5 * self.acceleration.x * CLOCK.get_elasped()**2) + (self.velocity.x * CLOCK.get_elasped())
dy = (0.5 * self.acceleration.y * CLOCK.get_elasped()**2) + (self.velocity.y * CLOCK.get_elasped())
return cur_pos.x + dx, cur_pos.y + dy
def run(self, seq_fasta_fn):
"""
Fold RNA with Nussinov algorithm.
Args:
seq_fasta_fn: path to fasta file containing sequence
Returns:
tuple of
(id_seq: fasta id of sequence,
seq: sequence,
structure: dot-bracket string of optimal folding)
"""
self.__evaluate_parameters(seq_fasta_fn)
self.__initialize()
self._compute_structures()
backtracking = NussinovBacktracking()
PredictionOutputData.structures = self._traceback(
Vector(self._tbl_len_x - 1, 0), backtracking)
self._create_structures()
self._output()
return (self._data.id, self._data.sequence,
PredictionOutputData.dot_bracket_structures[0])
def __init__(self, sprite_name, controller, pos):
BaseObject.__init__(self, sprite_name, pos, SPRITE_MANAGER.instance)
# assumes an already initialized controller
# TODO: Create virtual controller - currently we rely on PS3 controller
self.joystick = controller
self.land = False
self.can_shoot = 1
self.can_move = 1
self.trajectory = Vector(0, 0)
self.begun_movement = False # Could eliminate this by having the player already moving at start...
# TODO: get rid of this line of code, since we will be using a rect mask for collisions...
self.radius = self.rect.centerx - self.rect.x
self.old_hspeed, self.old_vspeed = 0, 0
self.hspeed, self.vspeed = 0, 0
self.fire_sound = load_sound("321102__nsstudios__laser1.wav")
self.health = HEALTH
self.bullet_group = GroupWithOwner(owner=self.name,
group_manager=BULLET_GROUP_MANAGER)
def _get_new_pos(self, trajectory):
new = self.pos - Vector(-trajectory[0], -trajectory[1])
self.pos += (new - self.pos).normal() * self.speed
return self.pos
def __init__(self):
self.updated_buttons = False
self.left_axis = Vector(0, 0)
self.right_axis = Vector(0, 0)
def getPlayerDirection(self):
rads = radians(self.facing_direction)
return Vector(sin(rads), cos(rads)).normal()
def getVelocity(self):
return Vector(self.velocity.x, self.velocity.y)
def getPosition(self):
return Vector(self.pos.x, self.pos.y)
def get_axes(self):
self.update_axis()
if self.left_axis is not None and self.right_axis is not None:
left = Vector(self.left_axis[0], self.left_axis[1])
right = Vector(self.right_axis[0], self.right_axis[1])
return left, right
def _get_neighbours(self, pos, input_data):
"""
Returns all neighbours
to which you can go from a matrix
cell.
Args:
pos: the position from which you want get all neighbours
input_data: the input for which you create the traceback
Returns:
neighbours of the cell at position pos
"""
neighbours = []
if pos.matrix_label == self.MATRIX_LBL_HORIZONTAL_GAPS:
return self.__get_neighbours_in_Q(pos, input_data)
elif pos.matrix_label == self.MATRIX_LBL_VERTICAL_GAPS:
return self.__get_neighbours_in_P(pos, input_data)
start = AlignmentOutputData.table_values[pos.y][pos.x]
diagonal = float(strings.NAN)
matrix_p = float(strings.NAN)
matrix_q = float(strings.NAN)
up = float(strings.NAN)
left = float(strings.NAN)
cur_char_seq_1 = strings.EMPTY
cur_char_seq_2 = strings.EMPTY
if pos.y - 1 >= 0 and pos.x - 1 >= 0:
diagonal = AlignmentOutputData.table_values[pos.y - 1][pos.x - 1]
if pos.y > 0:
matrix_p = AlignmentOutputData.table_vertical_gaps[pos.y][pos.x]
if pos.x > 0:
matrix_q = AlignmentOutputData.table_horizontal_gaps[pos.y][pos.x]
# marginal case
if pos.y - 1 >= 0 and pos.x == 0:
up = AlignmentOutputData.table_values[pos.y - 1][pos.x]
# marginal case
if pos.x - 1 >= 0 and pos.y == 0:
left = AlignmentOutputData.table_values[pos.y][pos.x - 1]
if pos.y - 1 >= 0:
cur_char_seq_1 = input_data.sequence_a[pos.y - 1]
if pos.x - 1 >= 0:
cur_char_seq_2 = input_data.sequence_b[pos.x - 1]
if cur_char_seq_1 != strings.EMPTY and cur_char_seq_2 != strings.EMPTY:
matching = start == diagonal + input_data.cost_function.get_value(cur_char_seq_1, cur_char_seq_2)
else:
matching = False
#matching = start == diagonal + (0 if cur_char_seq_1 == cur_char_seq_2 else -1)
change_to_p = start == matrix_p
change_to_q = start == matrix_q
# marginal cases
deletion = start == up + input_data.gap_beta
insertion = start == left + input_data.gap_beta
if matching:
neighbours.append(Vector(pos.x - 1, pos.y - 1).create(self.MATRIX_LBL_MAIN))
if change_to_p:
neighbours.append(Vector(pos.x, pos.y).create(self.MATRIX_LBL_VERTICAL_GAPS))
if change_to_q:
neighbours.append(Vector(pos.x, pos.y).create(self.MATRIX_LBL_HORIZONTAL_GAPS))
# marginal case
if insertion:
neighbours.append(Vector(pos.x - 1, pos.y).create(self.MATRIX_LBL_MAIN))
# marginal case
if deletion:
neighbours.append(Vector(pos.x, pos.y - 1).create(self.MATRIX_LBL_MAIN))
# marginal case
if not (matching or change_to_p or change_to_q or insertion or deletion) and (pos.x != 0 or pos.y != 0):
neighbours.append(Vector(0, 0).create(self.MATRIX_LBL_MAIN))
return neighbours