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remove redundant debug files for server smooth run
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@wang3702
wang3702 committed Dec 12, 2023
1 parent 439d5df commit 45a1543
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Showing 2 changed files with 59 additions and 46 deletions.
41 changes: 26 additions & 15 deletions graph/DP_geo_ops.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,22 +62,24 @@ def global_align_score(ldp_gap_penalty,match_matrix,
ldp_prev_connect[i]=prev_neighbor
return scratch,pointer,ldp_prev_connect

def dynamic_assign_geo(updated_base_list,ldp_gap_penalty,fragment_distance_array,save_path):
def dynamic_assign_geo(updated_base_list,ldp_gap_penalty,fragment_distance_array,save_path=None):
map_dict={0:"A",1:"T",2:"C",3:"G"}
match_matrix = np.max(updated_base_list,axis=1)#updated_base_list
score_path = os.path.join(save_path,"match_score.txt")
np.savetxt(score_path,match_matrix)
if save_path is not None:
score_path = os.path.join(save_path,"match_score.txt")
np.savetxt(score_path,match_matrix)
pointer = np.zeros(len(updated_base_list))#indicates the operations at position i
scratch = np.zeros(len(updated_base_list))
ldp_prev_connect = np.zeros(len(updated_base_list))-1
scratch,pointer,ldp_prev_connect=global_align_score(ldp_gap_penalty,match_matrix,
pointer, scratch,fragment_distance_array, ldp_prev_connect)
score_path = os.path.join(save_path,"optimal_score.txt")
np.savetxt(score_path,scratch)
score_path = os.path.join(save_path,"optimal_direction.txt")
np.savetxt(score_path,pointer)#verfied corret
score_path = os.path.join(save_path,"ldp_prev_connect.txt")
np.savetxt(score_path,ldp_prev_connect)
if save_path is not None:
score_path = os.path.join(save_path,"optimal_score.txt")
np.savetxt(score_path,scratch)
score_path = os.path.join(save_path,"optimal_direction.txt")
np.savetxt(score_path,pointer)#verfied corret
score_path = os.path.join(save_path,"ldp_prev_connect.txt")
np.savetxt(score_path,ldp_prev_connect)
input_seq_line=""
for i in range(len(updated_base_list)):
choice=int(np.argmax(updated_base_list[i]))
Expand All @@ -95,17 +97,26 @@ def dynamic_assign_geo(updated_base_list,ldp_gap_penalty,fragment_distance_array
max_score = np.max(scratch)
match_matrix = np.zeros(len(updated_base_list))
match_matrix[ldp_prev_connect==-1]=1
match_seq=""
with open(score_path,'w') as file:
file.write(input_seq_line+"\n")
if save_path is not None:
score_path = os.path.join(save_path,"match_seq.txt")
match_seq=""
with open(score_path,'w') as file:
file.write(input_seq_line+"\n")
for k in range(len(match_matrix)):
if match_matrix[k]==1:
file.write(input_seq_line[k])
match_seq +=input_seq_line[k]
else:
file.write("-")
match_seq+="-"
file.write("\n")
else:
match_seq=""
for k in range(len(match_matrix)):
if match_matrix[k]==1:
file.write(input_seq_line[k])
match_seq +=input_seq_line[k]
else:
file.write("-")
match_seq+="-"
file.write("\n")
return max_score,match_seq


Expand Down
64 changes: 33 additions & 31 deletions graph/DP_ops.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def global_align_score(ldp_gap,seq_gap, matrix, ldp_list,


def dynamic_assign_multi(updated_base_list,current_chain,
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array,save_path):
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array,save_path=None):
map_dict={0:"A",1:"T",2:"C",3:"G"}
#build M*N matrix
match_matrix = np.zeros([len(updated_base_list)+1,len(current_chain)+1])
Expand All @@ -114,8 +114,9 @@ def dynamic_assign_multi(updated_base_list,current_chain,
for j in range(len(current_chain)):
cur_label=int(current_chain[j])
match_matrix[i+1,j+1]=current_prob[cur_label]*100#-100#if it's higher than reference value, it should be bigger than 1
score_path = os.path.join(save_path,"match_score.txt")
np.savetxt(score_path,match_matrix)
if save_path is not None:
score_path = os.path.join(save_path,"match_score.txt")
np.savetxt(score_path,match_matrix)
match_score = match_matrix
pointer = np.zeros([len(updated_base_list)+1,len(current_chain)+1])
scratch = np.zeros([len(updated_base_list)+1,len(current_chain)+1])
Expand Down Expand Up @@ -145,18 +146,19 @@ def dynamic_assign_multi(updated_base_list,current_chain,
scratch,pointer,seq_gap_count,ldp_prev_connect,ldp_gap_count=global_align_score(ldp_gap_penalty,seq_gap_penalty, match_matrix,
np.arange(len(updated_base_list)), np.arange(len(current_chain)),
pointer, scratch,seq_gap_accumulation, ldp_gap_accumulation,fragment_final_distance, ldp_prev_connect,seq_gap_total_limit)
score_path = os.path.join(save_path,"optimal_score.txt")
np.savetxt(score_path,scratch)
score_path = os.path.join(save_path,"optimal_direction.txt")
np.savetxt(score_path,pointer)#verfied corret
score_path = os.path.join(save_path,"sequence_miss_count.txt")
np.savetxt(score_path,seq_gap_count)#verified correct
score_path = os.path.join(save_path,"ldp_prev_connect.txt")
np.savetxt(score_path,ldp_prev_connect)
score_path = os.path.join(save_path,"ldp_distance_array.txt")
np.savetxt(score_path,fragment_final_distance)
score_path = os.path.join(save_path,"ldp_gap_count.txt")
np.savetxt(score_path,ldp_gap_count)
if save_path is not None:
score_path = os.path.join(save_path,"optimal_score.txt")
np.savetxt(score_path,scratch)
score_path = os.path.join(save_path,"optimal_direction.txt")
np.savetxt(score_path,pointer)#verfied corret
score_path = os.path.join(save_path,"sequence_miss_count.txt")
np.savetxt(score_path,seq_gap_count)#verified correct
score_path = os.path.join(save_path,"ldp_prev_connect.txt")
np.savetxt(score_path,ldp_prev_connect)
score_path = os.path.join(save_path,"ldp_distance_array.txt")
np.savetxt(score_path,fragment_final_distance)
score_path = os.path.join(save_path,"ldp_gap_count.txt")
np.savetxt(score_path,ldp_gap_count)
input_seq_line=""
for i in range(len(updated_base_list)):
choice=int(np.argmax(updated_base_list[i]))
Expand Down Expand Up @@ -188,9 +190,9 @@ def dynamic_assign_multi(updated_base_list,current_chain,
cur_x -= int(abs(check_pointer))
#match_matrix[cur_x-1]=cur_y-1
check_pointer = pointer[cur_x,cur_y]

score_path = os.path.join(save_path,"match_result%d.txt"%count_match)
np.savetxt(score_path,match_matrix)
if save_path is not None:
score_path = os.path.join(save_path,"match_result%d.txt"%count_match)
np.savetxt(score_path,match_matrix)
match_seq_line = ""
count_replace =0
for i in range(len(match_matrix)):
Expand All @@ -216,15 +218,15 @@ def dynamic_assign_multi(updated_base_list,current_chain,
for i in range(len(current_chain)):
match_label = int(current_chain[i])
all_seq_line += map_dict[match_label]

score_path = os.path.join(save_path,"match_seq.txt")
with open(score_path,'w') as file:
file.write(input_seq_line+"\n")
for j in range(len(match_seq_list)):
current_interval = match_interval_list[j]
file.write(match_seq_list[j]+"\t"+"%.2f"%max_score_list[j]+
"\t%d,%d\n"%(current_interval[0],current_interval[1]))
file.write(all_seq_line+"\n")
if save_path is not None:
score_path = os.path.join(save_path,"match_seq.txt")
with open(score_path,'w') as file:
file.write(input_seq_line+"\n")
for j in range(len(match_seq_list)):
current_interval = match_interval_list[j]
file.write(match_seq_list[j]+"\t"+"%.2f"%max_score_list[j]+
"\t%d,%d\n"%(current_interval[0],current_interval[1]))
file.write(all_seq_line+"\n")

return max_score_list,match_seq_list,match_interval_list

Expand Down Expand Up @@ -296,7 +298,7 @@ def greedy_assign_PS(All_Base_Path_List_sugar,All_Path_List_sugar,Path_P_align_l
dp_save_path = os.path.join(cur_path_save_path,"path_starting_%d_chain_%s"%(start_ldp_index,current_chain_id))
mkdir(dp_save_path)
max_score, match_seq_line,match_seq_interval = dynamic_assign_multi(study_ldp_base_list,current_chain,
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, dp_save_path)
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, None)
path_assign_collection_list.extend(match_seq_line)
path_assign_score_list.extend(max_score)
path_assign_interval_list.extend(match_seq_interval)
Expand All @@ -306,7 +308,7 @@ def greedy_assign_PS(All_Base_Path_List_sugar,All_Path_List_sugar,Path_P_align_l
dp_save_path = os.path.join(cur_path_save_path,"rpath_starting_%d_chain_%s"%(start_ldp_index,current_chain_id))
mkdir(dp_save_path)
max_score, match_seq_line,match_seq_interval = dynamic_assign_multi(study_ldp_base_list,current_reverse_chain,
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, dp_save_path)
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, None)
path_assign_collection_list.extend(match_seq_line)
path_assign_score_list.extend(max_score)
path_assign_interval_list.extend(match_seq_interval)
Expand Down Expand Up @@ -383,7 +385,7 @@ def distributed_dp_calcu(chain_dict,cur_path_save_path,start_ldp_index,
dp_save_path = os.path.join(cur_path_save_path,"path_starting_%d_chain_%s"%(start_ldp_index,current_chain_id))
mkdir(dp_save_path)
max_score, match_seq_line,match_seq_interval = dynamic_assign_multi(study_ldp_base_list,current_chain,
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, dp_save_path)
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, None)
path_assign_collection_list.extend(match_seq_line)
path_assign_score_list.extend(max_score)
path_assign_interval_list.extend(match_seq_interval)
Expand All @@ -396,7 +398,7 @@ def distributed_dp_calcu(chain_dict,cur_path_save_path,start_ldp_index,
dp_save_path = os.path.join(cur_path_save_path,"rpath_starting_%d_chain_%s"%(start_ldp_index,current_chain_id))
mkdir(dp_save_path)
max_score, match_seq_line,match_seq_interval = dynamic_assign_multi(study_ldp_base_list,current_reverse_chain,
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, dp_save_path)
ldp_gap_penalty,seq_gap_penalty,fragment_distance_array, None)
path_assign_collection_list.extend(match_seq_line)
path_assign_score_list.extend(max_score)
path_assign_interval_list.extend(match_seq_interval)
Expand Down

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