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ContigS.py
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ContigS.py
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__author__ = 'hervemn'
from mutation import new_mutation as mutation
import numpy as np
class repeats():
def __init__(self):
""" initialization """
@classmethod
def init_from_initial_structure(cls, ContigS, contig_a, n_copy):
from copy import deepcopy as deepcopy
# duplicated bloc instance has an id which will be tracked
obj = cls()
obj.ContigS = ContigS
obj.name = contig_a.name
obj.init_contig = contig_a.composition[0]['init_contig']
obj.id_frag_start = contig_a.composition[0]['id_frag_start']
obj.id_frag_end = contig_a.composition[0]['id_frag_end']
obj.orientation = 'w'
obj.access_bloc = str(obj.id_frag_start)+':'+str(obj.id_frag_end)
print " access bloc = ",obj.access_bloc
obj.list_fragments = deepcopy(contig_a.FragmentS)
obj.current_positions = dict() # dictionnary of current positions of the duplicates
obj.incoming_connections = [] # list of new paste ( in the future split and paste)
obj.r_x = n_copy # number of repeats
obj.ContigS.init_contigs[obj.init_contig][obj.access_bloc]['dup'] = True # set this area as duplicated
obj.ContigS.inactivate(contig_a)
return obj
@classmethod
def init_from_previous_repeat(cls, old_repeat, ContigS):
from copy import deepcopy as deepcopy
""" initiate repeats and instances from previous data"""
obj = cls()
obj.ContigS = ContigS
obj.name = old_repeat.name
obj.init_contig = old_repeat.init_contig
obj.id_frag_start = old_repeat.id_frag_start
obj.id_frag_end = old_repeat.id_frag_end
obj.orientation = old_repeat.orientation
obj.access_bloc = old_repeat.access_bloc
obj.list_fragments = deepcopy(old_repeat.list_fragments)
# building translation dictionary from old instances to new instances
obj.current_positions = dict() # dictionnary of current positions of the duplicates
obj.incoming_connections = [] # list of new paste ( in the future split and paste)
obj.r_x = old_repeat.r_x # number of repeats
if not(obj.ContigS.init_contigs.has_key(obj.init_contig)):
obj.ContigS.init_contigs[obj.init_contig] = dict()
if not(obj.ContigS.init_contigs[obj.init_contig].has_key(obj.access_bloc)):
obj.ContigS.init_contigs[obj.init_contig][obj.access_bloc] = dict()
obj.ContigS.init_contigs[obj.init_contig][obj.access_bloc]['dup'] = True # set this area as duplicated
return obj
def add_position(self,id_instance,new_pos):
self.current_positions[id_instance] = new_pos
def is_instance_free(self,id_instance):
if self.current_positions[id_instance] == id_instance:
output = True
else:
output = False
return output
def remove_position(self,id_instance):
new_pos = dict()
new_pos['orientation'] = 'w'
new_pos['position'] = 1
new_pos['@'] = id_instance
self.current_positions[id_instance] = new_pos
def update_current_position(self, id_instance, new_pos):
"""update positions in class"""
self.current_positions[id_instance] = new_pos
def update_incoming_connections(self,connection):
""" add incoming connection """
def create_contig_instance(self,):
""" create instance from template"""
from copy import deepcopy as deepcopy
from contig import contig as contig
instance = contig.initiate(self.init_contig,self.id_frag_start,self.id_frag_end,self.orientation)
new_list_frag = deepcopy(self.list_fragments)
for frag in new_list_frag:
instance.append_fragment(frag,'w')
# print "frag current name = ",frag.curr_name
id_instance = self.ContigS.add(instance)
new_pos = dict()
new_pos['orientation'] = 'w'
new_pos['position'] = 1
new_pos['@'] = id_instance
instance.new_compo[0]["dup"] = True # importnat d etre defini apres
self.add_position(id_instance,new_pos)
return id_instance
def free_all_instances(self,):
""" destroy instances from template"""
class duplicator():
def __init__(self,ContigS):
""" initialization """
self.duplicated_blocs = dict()
self.ContigS = ContigS
self.incoming_connections = []
self.old_instance_2_new_instance = dict()
def define_repeat(self,C,pos_a,pos_b,n_copy):
""" """
from contig import contig as contig
# 1) definir le bloc duplique
# 2) l extraire = split x 2 + delete du bloc
# 3) creer une instance
# 4) inserer l'instance sa position initiale par paste
###################
out_split_a = self.ContigS.split(C,pos_a) # modifier split afin de mettre a jour duplicator : pas urgent/presque inutile
# print "name upstream bloc 1 = ",out_split_a['upstream']["contig"].name
# print "name downstream bloc 1 = ",out_split_a['downstream']["contig"].name
up_C = out_split_a['upstream']["contig"]
tmp_C = out_split_a['downstream']["contig"]
out_split_b = self.ContigS.split(C,pos_b)
dup_bloc = out_split_b['upstream']["contig"] # duplicated bloc
# print "name upstream bloc = ",out_split_b['upstream']["contig"].name
# print "name downstream bloc = ",out_split_b['downstream']["contig"].name
down_C = out_split_b['downstream']["contig"]
###################
repeat = repeats.init_from_initial_structure(self.ContigS, dup_bloc, n_copy)
self.duplicated_blocs[repeat.name] = repeat
for i in range(0,n_copy):
instance_repeat_id = repeat.create_contig_instance()
self.old_instance_2_new_instance[instance_repeat_id] = dict()
self.old_instance_2_new_instance[instance_repeat_id]["new_instance"] = instance_repeat_id
self.old_instance_2_new_instance[instance_repeat_id]["remapped"] = True
instance_repeat = self.ContigS.current_contigs[instance_repeat_id]
up_C_dup = self.ContigS.paste(up_C,'w',instance_repeat,'w') # modifier paste afin de mettre a jour duplicator
original = self.ContigS.paste(up_C_dup,'w',down_C,'w') # modifier paste afin de mettre a jour duplicator
# pop out reference to duplicated part in original contig
access_bloc_dup = str(pos_a + 1 ) +':' + str(pos_b) # be carefull of the split positions
C.old_2_new.pop(access_bloc_dup)
def define_repeat_from_old(self, old_repeat,):
repeat = repeats.init_from_previous_repeat(old_repeat,self.ContigS)
self.duplicated_blocs[repeat.name] = repeat
for ele in old_repeat.current_positions:
old_instance = ele
self.old_instance_2_new_instance[old_instance] = dict()
new_instance = repeat.create_contig_instance()
self.old_instance_2_new_instance[old_instance]["new_instance"] = new_instance
self.old_instance_2_new_instance[old_instance]["remapped"] = False
def delete_duplicated_bloc(self,dup):
""""""
def add_modification_to_network(self,incoming_connection):
self.incoming_connections.append(incoming_connection)
def path_generator(self):
""" return paste and split operations to perform on duplicated blocs"""
""" update current network """
class ContigS():
# from contig import contig as contig
def __init__(self):
import numpy as np
import contig as CONTI
self.duplicator = duplicator(self,)
self.current_contigs = dict() # dictionary of current contigs entry : 1 -- n_contigs
self.init_contigs = dict() # dictionnary of initial contigs : name given by de-novo assembler
self.g_sigma = dict() # dictionnary of initial fragments
self.np_id_2_frag = dict() # dictionary conversion of matrix index to init fragment name
self.n_contigs = 0 # number of contigs
self.size_current_genome = 0
# C-structures sent to GPU !
self.frag_T = np.dtype([('mult', np.int32), ('pos_min',np.int32), ('pos_max',np.int32), ('alpha',np.int32)], align = True)
self.coord_T = np.dtype([('chrom', np.int32),
('pos_kb', np.float32),
('low', np.int32),
('high', np.int32),
('circular', np.int32),
('id_rel', np.int32),
('size_contig', np.int32),
('cumul_index', np.int32),
('alpha', np.float32)], align=True)
self.alpha_collect_T = np.dtype([('obsd', np.float64), ('expd', np.float64)], align=True)
def compute_size_current_genome(self):
from contig import contig
size_current_genome = 0
for c in self.current_contigs.keys():
cont = self.current_contigs[c]
if isinstance(cont,contig):
if cont.status == 'active':
size_current_genome += cont.n_frags
self.size_current_genome = size_current_genome
def clear(self):
self.current_contigs.clear()
self.init_contigs.clear()
self.g_sigma.clear()
self.np_id_2_frag.clear()
self.n_contigs.clear()
def add_new_composite(self,contig):
from colorama import Fore, Back, Style
from colorama import init
init(autoreset=True)
from contig import contig as class_contig
""" perform adding of a contig which contain repeats"""
curr_contig = contig
pos_cut = 0
list_id_sub_contig = []
# for ele in contig.composition:
test_condition = True
curr_pos = 0
jump_bloc = True
while test_condition:
# for ele in curr_contig.composition:
ele = curr_contig.composition[curr_pos]
# variable pour sauter de contig
init_contig = ele["init_contig"]
access_bloc = str(ele["id_frag_start"])+':'+str(ele["id_frag_end"])
length_bloc = ele["id_frag_end"] - ele["id_frag_start"] + 1
# if not(self.init_contigs.has_key(init_contig)):
# self.init_contigs[init_contig] = dict()
if self.init_contigs[init_contig].has_key(access_bloc):
if self.init_contigs[init_contig][access_bloc]["dup"]:
bloc_upstream, tmp_bloc = class_contig.split(curr_contig,pos_cut)
# add bloc_upstream
if not(bloc_upstream.name == ''):
# print "name upstream = ",bloc_upstream.name
# print " new compo = ", bloc_upstream.new_compo
if bloc_upstream.has_repeats() and len(bloc_upstream.new_compo) ==1 :# <- check if has repeats!!!
# bloc_upstream.update_repeats(self.duplicator.old_instance_2_new_instance)
old_instance = bloc_upstream.new_compo[0]["contig_id"]
id_upstream = self.duplicator.old_instance_2_new_instance[old_instance]["new_instance"]
else:
id_upstream = self.add(bloc_upstream)
# self.current_contigs[id_upstream].new_compo[0]["contig_id"] = id_upstream
self.current_contigs[id_upstream].reset_old_2_new_new_compo()
list_id_sub_contig.append(id_upstream)
# print " tmp bloc name = ",tmp_bloc.name
if not(tmp_bloc.name == ''):
# print "name tmp = ",tmp_bloc.name
dup_bloc, bloc_downstream = class_contig.split(tmp_bloc, length_bloc)
# nouveau contig defini
curr_contig = bloc_downstream
curr_pos = 0
pos_cut = 0
if not(dup_bloc.name == ''):
if dup_bloc.has_repeats() and len(dup_bloc.new_compo) ==1:# <- check if has repeats!!!
old_instance = dup_bloc.new_compo[0]["contig_id"]
id_bloc_dup = self.duplicator.old_instance_2_new_instance[old_instance]["new_instance"]
# dup_bloc.update_repeats(self.duplicator.old_instance_2_new_instance)
else:
id_bloc_dup = self.add(dup_bloc)
# self.current_contigs[id_bloc_dup].new_compo[0]["contig_id"] = id_bloc_dup
self.current_contigs[id_bloc_dup].reset_old_2_new_new_compo()
list_id_sub_contig.append(id_bloc_dup)
else:
# nouveau contig defini
curr_contig = tmp_bloc
curr_pos = 0
pos_cut = 0
else:
pos_cut += length_bloc
curr_pos += 1
else:
curr_pos += 1
pos_cut += length_bloc
len_curr_cont = len(curr_contig.composition)
if curr_contig.name == '':
test_condition = False
else:
if (curr_pos <len_curr_cont):
test_condition = True
else:
test_condition = False
if not(curr_contig.name == '' ):
# print Fore.BLUE + " on est dedans!"
# print "name last contig = ", curr_contig.name
if curr_contig.has_repeats() and len(curr_contig.new_compo) == 1:# <- check if has repeats!!!
# curr_contig.update_repeats(self.duplicator.old_instance_2_new_instance)
old_instance = curr_contig.new_compo[0]["contig_id"]
id_bloc = self.duplicator.old_instance_2_new_instance[old_instance]["new_instance"]
else:
id_bloc = self.add(curr_contig)
# self.current_contigs[id_bloc].new_compo[0]["contig_id"] = id_bloc
self.current_contigs[id_bloc].reset_old_2_new_new_compo()
list_id_sub_contig.append(id_bloc)
curr_contig = self.current_contigs[id_bloc]
# print " length contig = ",curr_contig.n_frags
# print " last contig id = ", curr_contig.contig_id
output = self.current_contigs[list_id_sub_contig[0]]
len_sub_contig = len(list_id_sub_contig)
# print "list sub contig = ", list_id_sub_contig
# print " len sub contig = ", len_sub_contig
if len_sub_contig>1:
for i in range(1,len(list_id_sub_contig)):
sub_contig = list_id_sub_contig[i]
print Fore.BLUE + output.name
print Fore.RED + self.current_contigs[sub_contig].name
output_tmp = self.paste(output,'w',
self.current_contigs[sub_contig],'w')
output = output_tmp
return output.contig_id
def add(self,contig):
self.n_contigs +=1
# add contig into current_contigs dictionary
contig.update_name(self.n_contigs)
self.current_contigs[self.n_contigs] = contig
for fragment in contig.FragmentS:
# update np_id_2_frag
# fragment.update_name(self.n_contigs)
self.np_id_2_frag[fragment.np_id_abs] = fragment.init_name
# update g_sigma
if fragment.init_name in self.g_sigma:
self.g_sigma[fragment.init_name].add(fragment.curr_name)
else:
self.g_sigma[fragment.init_name] = set()
self.g_sigma[fragment.init_name].add(fragment.curr_name)
#update init_contigs
for ele in contig.composition:
init_contig = ele['init_contig']
if init_contig in self.init_contigs:
position = str(ele['id_frag_start'])+':' + str(ele['id_frag_end'])
if not(self.init_contigs[init_contig].has_key(position)):
self.init_contigs[init_contig][position] = dict()
self.init_contigs[init_contig][position]['dup'] = False
bloc_tag = str(ele['pos_id'])+'@'+str(contig.contig_id)
self.init_contigs[init_contig][position][bloc_tag] = str(ele['orientation'])
# is_duplicated = self.init_contigs[init_contig][position]['dup']
# if is_duplicated: # update duplicator structure
# name_repeat = '>'+init_contig+':'+position+':w>'
# repeat = self.duplicator.duplicated_blocs[name_repeat]
# repeat.add_position(bloc_tag)
else:
self.init_contigs[init_contig] = dict()
position = str(ele['id_frag_start'])+':'+str(ele['id_frag_end'])
self.init_contigs[init_contig][position] = dict()
bloc_tag = str(ele['pos_id'])+'@'+str(contig.contig_id)
self.init_contigs[init_contig][position][bloc_tag] = str(ele['orientation'])
self.init_contigs[init_contig][position]['dup'] = False # track de la signature de duplication
for ele in contig.new_compo:
if ele["dup"]:
position = ele["position"]
orientation = ele["orientation"]
tmp_id_instance = ele["contig_id"]
# id_instance must be renew only at the beginning
id_instance = tmp_id_instance
# if self.duplicator.old_instance_2_new_instance[tmp_id_instance]["remapped"]:
# id_instance = tmp_id_instance
# else:
# id_instance = self.duplicator.old_instance_2_new_instance[tmp_id_instance]["new_instance"]
# self.duplicator.old_instance_2_new_instance[tmp_id_instance]["remapped"] = True
## self.duplicator.old_instance_2_new_instance[id_instance]["new_instance"] = id_instance
print "id instance = ", id_instance
ele["contig_id"] = id_instance
self.inactivate(self.current_contigs[id_instance]) # desactivation : dans tous les cas il est rajoute
name_repeat = self.current_contigs[id_instance].name # problem when going from genome t to genome ( t+1 )
repeat = self.duplicator.duplicated_blocs[name_repeat]
new_pos = dict()
new_pos['orientation'] = orientation
new_pos['position'] = position
new_pos['@'] = self.n_contigs
repeat.update_current_position(id_instance,new_pos)
self.compute_size_current_genome()
return self.n_contigs
def create_transparent_contig(self,):
from contig import contig as contig
transpa = contig.initiate("None",0,0,"w")
return transpa
def export_name_contigs(self,):
out = []
for ele in self.current_contigs:
curr_cont = self.current_contigs[ele]
if curr_cont.status == "active":
out.append(curr_cont.name)
return out
def print_active_contig(self):
from colorama import Fore, Back, Style
from colorama import init
init(autoreset=True)
print Fore.BLUE + "list active contig"
print "-----------------"
for ele in self.current_contigs:
curr_cont = self.current_contigs[ele]
if curr_cont.status == "active":
print Fore.RED + str(curr_cont.contig_id) + Fore.WHITE +" ==> " + Fore.GREEN + curr_cont.name
print "-----------------"
init(autoreset=True)
####################################################################################
################# basic mutations paste split duplicate inactivate activate ########
def inactivate(self, contig):
if self.current_contigs[contig.contig_id].status == 'active':
# print " on va inactiver les fragments et les retirer de g sigma. contig id = ",contig.contig_id
for fragment in contig.FragmentS:
# print " fragment curr name = " ,fragment.curr_name
# print " contenu g sigma = ", self.g_sigma[fragment.init_name]
# print "removing : ", fragment.curr_name
self.g_sigma[fragment.init_name].remove(fragment.curr_name)
try:
self.np_id_2_frag.pop(fragment.np_id_abs) # attention ....
except:
""
for ele in contig.composition:
init_contig = ele['init_contig']
position = str(ele['id_frag_start'])+':'+str(ele['id_frag_end'])
bloc_tag = str(ele['pos_id'])+'@'+str(contig.contig_id)
self.init_contigs[init_contig][position].pop(bloc_tag)
if self.init_contigs[init_contig][position] == {'dup':False}:
self.init_contigs[init_contig].pop(position)
for ele in contig.new_compo:
if ele["dup"]:
id_instance = ele["contig_id"]
# print "id instance = ", id_instance
name_repeat = self.current_contigs[id_instance].name
# print " name repeat = ", name_repeat
repeat = self.duplicator.duplicated_blocs[name_repeat]
repeat.remove_position(id_instance)
self.current_contigs[contig.contig_id].status = 'inactive'
self.compute_size_current_genome()
def reactivate(self,contig):
if self.current_contigs[contig.contig_id].status == 'inactive':
contig.status = 'active'
for fragment in contig.FragmentS:
# update np_id_2_frag
fragment.update_name(self.n_contigs)
self.np_id_2_frag[fragment.np_id_abs] = fragment.init_name
# update g_sigma
if self.g_sigma.has_key(fragment.init_name):
self.g_sigma[fragment.init_name].add(fragment.curr_name)
else:
self.g_sigma[fragment.init_name] = set()
self.g_sigma[fragment.init_name].add(fragment.curr_name)
#update init_contigs
for ele in contig.composition:
init_contig = ele['init_contig']
if self.init_contigs.has_key(init_contig):
position = str(ele['id_frag_start'])+':'+str(ele['id_frag_end'])
if not(self.init_contigs[init_contig].has_key(position)):
self.init_contigs[init_contig][position] = dict()
self.init_contigs[init_contig][position]["dup"] = False # added 23 /02 /2013
bloc_tag = str(ele['pos_id'])+'@'+str(contig.contig_id)
self.init_contigs[init_contig][position][bloc_tag] = str(ele['orientation'])
else:
self.init_contigs[init_contig] = dict()
position = str(ele['id_frag_start'])+':'+str(ele['id_frag_end'])
self.init_contigs[init_contig][position] = dict()
self.init_contigs[init_contig][position]['dup'] = False
bloc_tag = str(ele['pos_id'])+'@'+str(contig.contig_id)
self.init_contigs[init_contig][position][bloc_tag] = str(ele['orientation'])
for ele in contig.new_compo:
if ele["dup"]:
position = ele["position"]
orientation = ele["orientation"]
id_instance = ele["contig_id"]
name_repeat = self.current_contigs[id_instance].name
repeat = self.duplicator.duplicated_blocs[name_repeat]
new_pos = dict()
new_pos['orientation'] = orientation
new_pos['position'] = position
new_pos['@'] = contig.contig_id
repeat.add_position(id_instance,new_pos)
self.compute_size_current_genome()
return self.n_contigs
def duplicate(self,contig_a, pos_a,pos_b):
from contig import contig as contig
print "duplicate"
test_a = pos_a>=1
test_b = pos_b<=contig_a.n_frags
if test_a and test_b:
print "duplication possible"
bloc_duplicated = contig.duplicate(contig_a,pos_a,pos_b)
for ele in bloc_duplicated.new_compo:
ele['dup'] = True
id_bloc = self.add(bloc_duplicated)
else:
print "duplication impossible"
id_bloc = 0
return self.current_contigs[id_bloc]
def sort_blocs_in_old_2_new(self,contig_a):
sub_parts_tmp = contig_a.old_2_new.keys()
dico_tmp = dict()
for ele in sub_parts_tmp:
bla = int(ele.split(':')[0])
dico_tmp[bla] = ele
tmp_sub=[]
tmp_sub.extend(dico_tmp.keys())
tmp_sub.sort()
sub_parts = []
for ele in tmp_sub:
sub_parts.append(dico_tmp[ele])
return sub_parts
def pos_in_bloc_2_global_pos(self,contig,pos_in_bloc,bloc_id):
output = dict()
t = range(0,bloc_id - 1)
cumul_length = 0
print "contig new compo = ", contig.new_compo
print "contig name = ", contig.name
print "pos in bloc :", pos_in_bloc
print "bloc id = ", bloc_id
for h in t:
start = contig.new_compo[h]['start']
end = contig.new_compo[h]['end']
len_bloc = end - start + 1
cumul_length += len_bloc
start = contig.new_compo[bloc_id - 1]['start']
end = contig.new_compo[bloc_id - 1]['end']
len_bloc = end - start + 1
orientation = contig.new_compo[bloc_id - 1]["orientation"]
if orientation == 'w':
output["reverse_order"] = False
new_pos = cumul_length + pos_in_bloc
output["new_pos"] = new_pos
output["orientation"] = 'w'
else:
new_pos = cumul_length + (len_bloc - pos_in_bloc) + 1
output["reverse_order"] = True
output["new_pos"] = new_pos - 1 # because split will take the upper part of the contig
output["orientation"] = 'c'
return output
def find_new_position(self, contig_a, pos_a):
sorted_blocs = self.sort_blocs_in_old_2_new(contig_a)
output = dict()
output["upstream"] = dict()
output["downstream"] = dict()
output["safe_split"] = True
output["classic"] = dict()
i = 0
sum_size_previous_blocs = 0
size_previous_blocs = [0]
print "pos_a = ", pos_a
print "sorted blocs = "
print sorted_blocs
for ele in sorted_blocs:
print "sub parts = ", ele
tmp = ele.split(':')
low_lim = int(tmp[0])
high_lim = int(tmp[1])
size_bloc = high_lim - low_lim + 1
pos_in_bloc = pos_a - sum_size_previous_blocs
is_good_bloc = (pos_a >= low_lim and pos_a <= high_lim) or ((pos_a == 0) and (i ==0) )
# test if pos fall into a duplicated bloc ...
if is_good_bloc:
is_on_edge = False
if pos_a == high_lim:
print "output complex"
output["safe_split"] = False
cont_up_id = contig_a.old_2_new[ele]['contig_id']
up_bloc_id = contig_a.old_2_new[ele]['position']
cont_up = self.current_contigs[cont_up_id]
print "pos in bloc = ", pos_in_bloc
out_up = self.pos_in_bloc_2_global_pos(cont_up,pos_in_bloc,up_bloc_id)
output["upstream"]["bloc"] = ele
output["upstream"]["contig"] = cont_up
output["upstream"]["cut_info"] = out_up
output["upstream"]["exists"] = True
if i == len(sorted_blocs) - 1: # l index dnas les sorted blocs va de 0 a len -1
output["downstream"]["exists"] = False
output["downstream"]["bloc"] = "none"
output["downstream"]["contig"] = "none"
output["downstream"]["cut_info"] = "none"
else:
#find downstream
down_bloc = sorted_blocs[i + 1]
output["downstream"]["exists"] = True
output["downstream"]["bloc"] = down_bloc
cont_down_id = contig_a.old_2_new[down_bloc]['contig_id']
down_bloc_id = contig_a.old_2_new[down_bloc]['position']
cont_down = self.current_contigs[cont_down_id]
# pos_in_bloc_downstream = (pos_a + 1) - (sum_size_previous_blocs + size_bloc)
pos_in_bloc_downstream = 0
out_down = self.pos_in_bloc_2_global_pos(cont_down,pos_in_bloc_downstream,down_bloc_id)
output["downstream"]["bloc"] = down_bloc
output["downstream"]["contig"] = cont_down
output["downstream"]["cut_info"] = out_down
elif pos_a == 0:
print "output complex"
output["safe_split"] = False
cont_down_id = contig_a.old_2_new[ele]['contig_id']
down_bloc_id = contig_a.old_2_new[ele]['position']
cont_down = self.current_contigs[cont_down_id]
print "pos in bloc = ",pos_in_bloc
out_down = self.pos_in_bloc_2_global_pos(cont_down,pos_in_bloc,down_bloc_id)
output["downstream"]["bloc"] = ele
output["downstream"]["contig"] = cont_down
output["downstream"]["cut_info"] = out_down
output["downstream"]["exists"] = True
output["upstream"]["exists"] = False
output["upstream"]["bloc"] = "none"
output["upstream"]["contig"] = "none"
output["upstream"]["cut_info"] = "none"
else:
print "output classic"
data_bloc = contig_a.old_2_new[ele]
bloc_id = data_bloc['position']
contig_id = data_bloc['contig_id']
contig_to_split = self.current_contigs[contig_id]
output["classic"]["contig"] = contig_to_split
print "ele"
output["classic"]["bloc"] = ele
status = contig_to_split.status
# if status == 'active':
print " successful candidate to split = ", contig_to_split.name
out_classic = self.pos_in_bloc_2_global_pos(contig_to_split,pos_in_bloc,bloc_id)
output["classic"]["cut_info"] = out_classic
i +=1
sum_size_previous_blocs += size_bloc
size_previous_blocs.append(size_bloc)
return output
def post_split_update(self,contig_a, contig_1, contig_2):
# print "inactivate contig = ",contig_a.contig_id
self.inactivate(contig_a)
id_1 = self.add(contig_1)
id_2 = self.add(contig_2)
for ele in self.current_contigs[id_1].new_compo:
if (ele['dup']): # update duplicator and repeat object
position = ele["position"]
orientation = ele["orientation"]
id_instance = ele["contig_id"]
name_repeat = self.current_contigs[id_instance].name
repeat = self.duplicator.duplicated_blocs[name_repeat]
new_pos = dict()
new_pos['orientation'] = orientation
new_pos['position'] = position
new_pos['@'] = id_1
repeat.update_current_position(id_instance,new_pos)
start = ele['start']
end = ele['end']
pos = str(start)+':'+str(end)
self.current_contigs[ele['contig_id']].old_2_new[pos] = {'contig_id':id_1,'position':ele['position'],'orientation':ele['orientation']}
tmp_n_frags = self.current_contigs[ele['contig_id']].n_frags
pos_all = '1:'+str(tmp_n_frags)
for ele in self.current_contigs[id_2].new_compo:
if (ele['dup']): # update duplicator and repeat object
position = ele["position"]
orientation = ele["orientation"]
id_instance = ele["contig_id"]
name_repeat = self.current_contigs[id_instance].name
repeat = self.duplicator.duplicated_blocs[name_repeat]
new_pos = dict()
new_pos['orientation'] = orientation
new_pos['position'] = position
new_pos['@'] = id_2
repeat.update_current_position(id_instance,new_pos)
start = ele['start']
end = ele['end']
pos = str(start)+':'+str(end)
self.current_contigs[ele['contig_id']].old_2_new[pos] = {'contig_id':id_2,'position':ele['position'],'orientation':ele['orientation']}
tmp_n_frags = self.current_contigs[ele['contig_id']].n_frags
pos_all = '1:'+str(tmp_n_frags)
return id_1, id_2
def genome_2_abs_frag_vect(self):
abs_frag_vect = []
list_key = self.current_contigs.keys()
list_key.sort()
for contig in list_key:
if self.current_contigs[contig].status == 'active':
# be carefull with duplicated elements
abs_frag_vect.extend(self.current_contigs[contig].export_abs_frag_vect())
return abs_frag_vect
def export_kb_pos_and_ctg_id(self):
kb_pos_and_ctg_id = []
list_key = self.current_contigs.keys()
list_key.sort()
for contig in list_key:
if self.current_contigs[contig].status == 'active':
kb_pos_and_ctg_id.extend(self.current_contigs[contig].export_kb_pos_and_ctg_id())
return kb_pos_and_ctg_id
def extract_info_frag(self,fragment_name):
import numpy as np
# print fragment_name
data = fragment_name.split('-')
id_frag = np.int32(data[0])
contig_id =np.int32(int(data[1]))
pos_kb = np.int32(int(float(data[2]) ))
return id_frag, contig_id,pos_kb
def export_pos_frag(self,):
"deprecated"
import numpy as np
ind = -1
pos_frag = []
pos_frag.extend(self.np_id_2_frag.keys())
pos_frag.sort()
index_frag = np.zeros(len(pos_frag),dtype=np.int32)
frag_multi_pos = []
for np_frag in pos_frag:
init_frag = self.np_id_2_frag[np_frag]
multi_frags = self.g_sigma[init_frag]
for ele in multi_frags:
id_frag,contig_id,pos_kb = self.extract_info_frag(ele)
frag_multi_pos.extend([int(pos_kb),int(contig_id)])
ind +=2
# print np_frag
index_frag[np_frag-1] = ind
frag_multi_pos_np = np.array(frag_multi_pos,dtype=np.int32)
return index_frag,frag_multi_pos_np
def export_dico_frags_per_contig(self,):
import numpy as np
output_dico = dict()
for contg in self.current_contigs.keys():
tmp_ctg = self.current_contigs[contg]
tmp_frag_np = []
for frag in tmp_ctg.FragmentS:
tmp_frag_np.append(frag.np_id_abs - 1)
output_dico[contg] = np.array(tmp_frag_np,dtype = np.int32)
return output_dico
def export_index_matrix(self,):
out_np_index = []
out_np_ori = []
out_dup = []
n_frags = len(self.np_id_2_frag)
rev_np_index = np.zeros((n_frags), dtype=np.int32)
out_np_index = np.zeros((n_frags), dtype=np.int32)
new_id = 0
for ele in self.current_contigs:
cont = self.current_contigs[ele]
if cont.status == "active":
k = 0
for ele in cont.FragmentS:
np_id = ele.np_id_abs - 1
orientation = ele.orientation
bloc = self.return_bloc(cont, k + 1)
init_contig = ele.init_contig
# print "init contig = ",init_contig
is_duplicated = self.init_contigs[init_contig][bloc]['dup']
if is_duplicated:
out_dup.append(1)
else:
out_dup.append(0)
out_np_index[new_id] = np_id
out_np_ori.append(orientation)
rev_np_index[np_id] = new_id
k += 1
new_id += 1
return out_np_index, rev_np_index, out_np_ori
def clean_current_contigs(self,):
list_contigs = self.current_contigs.keys()
for c in list_contigs:
if self.current_contigs[c].status =='inactive':
self.current_contigs.pop(c)
def export_pos_frag_2_np_cl(self,):
import numpy as np
from contig import contig as contig
dico_contigs = dict()
length_contigs = []
rev_dict = dict()
list_contigs = self.current_contigs.keys()
# list_contigs.sort()
for c in list_contigs:
cont = self.current_contigs[c]
if isinstance(cont,contig):
if cont.status == 'active':
length_contigs.append(cont.n_frags)
dico_contigs[cont.contig_id] = dict()
dico_contigs[cont.contig_id]['length'] = cont.n_frags
# rel pos = position relative du contig dans la liste des contigs actifs
rel_pos = len(length_contigs) - 1
dico_contigs[cont.contig_id]['rel_pos'] = rel_pos
rev_dict[rel_pos] = cont.contig_id
# else:
# self.current_contigs.pop(c)
tmp_cumulu = ( (length_contigs[0] +1)*length_contigs[0])/2
dico_contigs[rev_dict[0]]['cumul_index'] = 0
dico_contigs[rev_dict[0]]['cumul_index_max'] = tmp_cumulu - 1
prec = tmp_cumulu
for i in xrange(1,len(length_contigs)):
dico_contigs[rev_dict[i]]['cumul_index'] = prec
cumulu = ((length_contigs[i] +1)*length_contigs[i]) / 2
tmp_cumulu = prec + cumulu
dico_contigs[rev_dict[i]]['cumul_index_max'] =tmp_cumulu -1
prec = tmp_cumulu
# on considere que les virtua contigs sont ordonnes ...
pos_frag = []
pos_frag.extend(self.np_id_2_frag.keys())
pos_frag.sort()
frag_coord_pos = []
frag_list = []
# construction dtype collect alpha contigs to do later!!!
alpha_collect = []
for i in xrange(0,len(length_contigs)):
cumulu = np.int32(((length_contigs[i] +1)*length_contigs[i])) / np.int32(2)
alpha_collect.append(cumulu)
id = 0
for np_frag in pos_frag:
init_frag = self.np_id_2_frag[np_frag]
multi_frags = self.g_sigma[init_frag]
n_multi_frag = len(multi_frags)
pos_data_0 = id
for ele in multi_frags:
id += 1
curr_id_frag, contig_id, pos_kb = self.extract_info_frag(ele)
low = self.current_contigs[contig_id].FragmentS[0].np_id_abs - 1
high = self.current_contigs[contig_id].FragmentS[-1].np_id_abs - 1
id_frag_rel = curr_id_frag - 1
circular = 0
size_contig = dico_contigs[contig_id]['length']
# print "size contig = ",size_contig
cumul_index = dico_contigs[contig_id]['cumul_index']
alpha = 0
frag_coord_pos.append((np.int32(contig_id),
np.float32(pos_kb),
np.int32(low),
np.int32(high),
np.int32(circular),
np.int32(id_frag_rel),
np.int32(size_contig),
np.int32(cumul_index),
np.float32(alpha)))
pos_data_1 = id - 1
frag_list.append((np.int32(n_multi_frag), np.int32(pos_data_0), np.int32(pos_data_1),np.int32(0)))
frag_multi_pos_np = np.array(frag_coord_pos,dtype=self.coord_T)
frag_list_np = np.array(frag_list,dtype = self.frag_T)
alpha_collect = np.array(alpha_collect)
n_alpha = alpha_collect.sum()
alpha_collect_np = np.zeros( (n_alpha,), dtype=self.alpha_collect_T)
# print "n element alpha collect = ", alpha_collect.sum()
# print "size np alpha collect = ", alpha_collect_np.shape
# print "n alpha = ", n_alpha
# for ele in range(0,n_alpha):
# alpha_collect_np[ele]['obsd'] = np.float64(0)
# alpha_collect_np[ele]['expd'] = np.float64(0)
return frag_list_np, frag_multi_pos_np, alpha_collect_np, dico_contigs
def candidate_deletion(self,contig_a):
# modifiable : augmente duplicated blocs en rajoutant les combinaison possible de bloc existant !!!
# homogeneite : meme contig initial et meme niveau de multiplication
# version actuelle: destruction des blocs homogenes de contigs
# pour la mutation inverse il suffit d aller dans le dictionnaire des contigs initiaux et de prendre un candidat para ceux existant !!!
print "scan contig to find possible deletion"
pos_duplication = []
FragS = contig_a.FragmentS
for frag in FragS:
data = self.g_sigma[frag.init_name]
n_repeats = data.__len__()
init_contig = frag.init_contig
id_init = frag.id_init
orientation = frag.orientation
pos_duplication.append([n_repeats, init_contig, id_init,orientation])
tmp = []
duplicated_blocs = []
prec_n_repeats = pos_duplication[0][0]
prec_init_contig = pos_duplication[0][1]
prec_id_init = pos_duplication[0][2]
prec_orientation = pos_duplication[0][3]
for i in range(0,len(pos_duplication)):
n_repeats = pos_duplication[i][0]
init_contig = pos_duplication[i][1]
id_init = pos_duplication[i][2]
orientation = pos_duplication[i][3]
test1 = n_repeats>1
test2 = init_contig == prec_init_contig
test3 = orientation == prec_orientation
test4 = orientation == 'w'
test5 = not(n_repeats == prec_n_repeats)
if test1:
if test2:
dif_id = id_init - prec_id_init
if (dif_id == 0) or abs(dif_id>1) or not(test3) or (test5):
if len(tmp)>0:
duplicated_blocs.append([min(tmp) + 1 , max(tmp) + 1 ])
tmp = []
else:
tmp.append(i)
elif (dif_id == -1) and test3 and test4:
if len(tmp)>0:
duplicated_blocs.append([min(tmp) + 1 , max(tmp) + 1 ])
tmp = []
else:
tmp.append(i)
elif (dif_id) == 1 and test3 and not(test4):
if len(tmp)>0:
duplicated_blocs.append([min(tmp) + 1 , max(tmp) + 1 ])
tmp = []
else:
tmp.append(i)
else:
tmp.append(i)
else:
if len(tmp)>0:
duplicated_blocs.append([min(tmp) + 1 , max(tmp) + 1 ])
tmp = []
else:
tmp.append(i)
else:
if len(tmp)>0:
duplicated_blocs.append([min(tmp) + 1 , max(tmp) + 1 ])
tmp = []
prec_n_repeats = n_repeats
prec_id_init = id_init
prec_init_contig = init_contig
prec_id_init = id_init
prec_orientation = orientation
return duplicated_blocs
########################################################################################################################
########################################################################################################################
def opposite_or(self,orientation):