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create_synteny_matrix.py

@@ -9,7 +9,8 @@ from skbio.alignment import local_pairwise_align_ssw
 from skbio import DNA,TabularMSA,RNA
 
 def update(gene_seq,gene):
-    while(1):
+    t=0
+    while(t!=100):
         try:
             server = "https://rest.ensembl.org"
             ext = "/sequence/id/"+str(gene)+"?type=cds;multiple_sequences=1"
@@ -36,8 +37,10 @@ def update(gene_seq,gene):
                 gene_seq[gene]=str(r["seq"])
                 return
         except Exception as e:
+            t+=1
             print("\nError:",e)
             continue
+    gene_seq[gene]=""
 
 def create_synteny_matrix_mul(gene_seq,g1,g2,n):
     for gene in g1:
@@ -46,7 +49,7 @@ def create_synteny_matrix_mul(gene_seq,g1,g2,n):
         try:
             temp=gene_seq[gene]
         except:
-            print("Updating gene sequences for gene:",gene)
+            #print("Updating gene sequences for gene:",gene)
             update(gene_seq,gene)
     for gene in g2:
         if gene=="NULL_GENE":
@@ -54,7 +57,7 @@ def create_synteny_matrix_mul(gene_seq,g1,g2,n):
         try:
             temp=gene_seq[gene]
         except:
-            print("Updating gene sequences for gene:",gene)
+            #print("Updating gene sequences for gene:",gene)
             update(gene_seq,gene)
     #print(n)
     sm=np.zeros((n,n,2))
@@ -75,7 +78,6 @@ def create_synteny_matrix_mul(gene_seq,g1,g2,n):
                 sml[i][j][0]=result/(norm_len)
                 _,result,_=local_pairwise_align_ssw(DNA(gene_seq[g1[i]]),DNA(gene_seq[g2[j]][::-1]))
                 sml[i][j][1]=result/(norm_len)
-
             except:
                 return np.zeros((n,n,2)),np.zeros((n,n,2))
     return sm,sml

get_data.py

@@ -36,21 +36,21 @@ def get_data_genome(arg,dir):
 def get_data_homology(arg,dir):
     a_h=[]
     d_h={}
-    if arg[2]=="-l":
+    if arg[0]=="-l":
         if not os.path.exists(dir):
             os.mkdir(dir)
-        download_data(arg[3],dir)
-    elif arg[2]=="-f":
-        get_data_file(arg[3],dir)
-    elif arg[2]=="-d":
-        if arg[4]=="-r":
+        download_data(arg[1],dir)
+    elif arg[0]=="-f":
+        get_data_file(arg[1],dir)
+    elif arg[0]=="-d":
+        if arg[2]=="-r":
             c=0
         else:
             return a_h,d_h
     elif arg[2]=="-nd":
         return a_h,d_h
 
-    if arg[4]=="-r":
+    if arg[2]=="-r":
         a_h,d_h=read_data_homology(dir)
         assert(len(a_h)==len(d_h))
 

prepare_negative_dataset.py

@@ -5,6 +5,7 @@ import os
 import gc
 import progressbar
 import random
+import pickle
 from read_data import read_data_homology,read_data_genome
 
 arg=sys.argv
@@ -23,9 +24,12 @@ for df in progressbar.progressbar(a_h):
     for h in hgids:
         gmap[h]=1
 
-a=[]
-d={}
-a,d=read_data_genome("data",a,d)
+data={}
+with open("genome_maps","rb") as file:
+    data=pickle.load(file)
+a=data["a"]
+d=data["d"]
+data={}
 assert(len(a)==len(d))
 indexes_gd=[list(df.index.values) for df in a]
 d=list(d.keys())

prepare_other_features_negative.py

@@ -0,0 +1,55 @@
+import pandas as pd
+import numpy as np 
+import json
+import gc
+import pickle
+import progressbar
+import sys
+from tree_data import create_tree_data
+
+
+
+smg_name="negative_dataset_synteny_matrices_global"
+sml_name="negative_dataset_synteny_matrices_local"
+smi_name="negative_dataset_indexes"
+dir_name="processed/synteny_matrices/"
+label=2
+
+rows=[]
+df=pd.read_hdf("negative_dataset.h5",key="ndf")
+try:
+    smg=np.load(dir_name+smg_name+".npy")
+    sml=np.load(dir_name+sml_name+".npy")
+    indexes=np.load(dir_name+smi_name+".npy")
+except:
+    print("Incomplete data")
+    sys.exit(1)
+df=df.loc[indexes]
+for _,row in progressbar.progressbar(df.iterrows()):
+    row["homology_species"]=row["homology_species"].lower()
+branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs=create_tree_data("species_tree.tree",df)
+assert(len(branch_length_species)==len(df))
+assert(len(sml)==len(distance))
+for i in range(len(df)):
+    index=indexes[i]
+    row=df.loc[index]
+    r={}
+    r["species"]=row["species"]
+    r["homology_species"]=row["homology_species"]
+    r["gene_stable_id"]=row["gene_stable_id"]
+    r["homology_gene_stable_id"]=row["homology_gene_stable_id"]
+    r["label"]=label
+    r["global_alignment_matrix"]=smg[i]
+    r["local_alignment_matrix"]=sml[i]
+    r["index_homology_dataset"]=index
+    r["bls"]=branch_length_species[i]
+    r["blhs"]=branch_length_homology_species[i]
+    r["dis"]=distance[i]
+    r["dps"]=dist_p_s[i]
+    r["dphs"]=dist_p_hs[i]
+    rows.append(r)
+
+with open("negative_dataset","wb") as file:
+    pickle.dump(rows,file)
+
+print("Data Saved Successfully:)")

prepare_synteny_matrix_negative.py

@@ -13,7 +13,6 @@ if not os.path.isdir("processed/synteny_matrices"):
 df=pd.read_hdf("negative_dataset.h5",key="ndf")
 for _,row in progressbar.progressbar(df.iterrows()):
     row["homology_species"]=row["homology_species"].lower()
-print(df[0:10])
 
 with open("processed/neighbor_genes.json","r") as file:
     lsy=dict(json.load(file))
@@ -22,21 +21,16 @@ print("Neighbor Genes Loaded")
 
 a_h=[]
 a_h.append(df)
-#gene_sequences=read_gene_sequences(a_h,lsy,"geneseq","gene_sequences")
-with open("processed/gene_sequences.json","r") as file:
-    gene_sequences=dict(json.load(file))
+gene_sequences=read_gene_sequences(a_h,lsy,"geneseq","gene_sequences")
 print("Gene Sequences Loaded")
 
-
-
 n=3
 ndir="processed/synteny_matrices/"
 nf1="synteny_matrices_global"
 nf2="synteny_matrices_local"
 nf3="indexes"
-for i in range(10):
-    synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,df[i*100000:(i+1)*100000],lsy,n,0)
-    np.save(ndir+"negative_dataset"+"_"+nf1+str(i),synteny_matrices_global)
-    np.save(ndir+"negative_dataset"+"_"+nf2+str(i),synteny_matrices_local)
-    np.save(ndir+"negative_dataset"+"_"+nf3+str(i),indexes)
+synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,df,lsy,n,0)
+np.save(ndir+"negative_dataset"+"_"+nf1,synteny_matrices_global)
+np.save(ndir+"negative_dataset"+"_"+nf2,synteny_matrices_local)
+np.save(ndir+"negative_dataset"+"_"+nf3,indexes)
 print("Synteny Matrices Created Successfully :)")

read_data.py

@@ -36,7 +36,8 @@ def read_data_genome(dir_name,a,dict_ind_genome):
         except:
             continue
         #print(data_gene[0:10])        
-        data_gene=data_gene[data_gene['gene_biotype']=='protein_coding']
+        data_gene=data_gene[(data_gene['gene_biotype']=='protein_coding') | (data_gene['gene_source']=='protein_coding')]
+        #print(data_gene[data_gene["gene_id"]=="ENSPMGG00000022088"])
         a.append(data_gene)
         n=lf[x].split(".")[0]
         dict_ind_genome[n]=len(a)-1

update_neighbor_genes_ndf.py

@@ -8,23 +8,6 @@ import pickle
 from get_data import get_data_homology,get_data_genome
 from process_data import create_data_homology_ls
 
-if not os.path.exists("processed"):
-    os.mkdir("processed")
-
-arg=sys.argv
-arg=arg[1:]
-
-enable_break=0
-
-if arg[-1]=="-test":
-    enable_break=1
-
-arg=arg[:-1]
-
-if len(arg)!=3:
-    print("No. of arguments more or less. Please check")
-    sys.exit(1)
-
 data={}
 with open("genome_maps","rb") as file:
     data=pickle.load(file)
@@ -45,6 +28,6 @@ print("Data Read")
 n=3 #no. of numbers neighbors
 save_after=5 #to save data after n steps
 
-lsy=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg,cmap,cimap,save_after,enable_break)
+lsy=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg,cmap,cimap,save_after,0)
 print(len(lsy))
 print("Neighbor Genes Updated Successfully")