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main.py

@@ -1,6 +1,7 @@
 import sys
 
 from get_data import get_data_homology,get_data_genome
+from process_data import create_data_homology_ls
 
 arg=sys.argv
 arg=arg[1:]
@@ -18,10 +19,24 @@ ldg=[]
 dir_g="data"
 
 ld,ldg,a,d=get_data_genome(arg,dir_g,a,d,ld,ldg)
-#print(a[0][0:10],"\n",a[2][0:10],"\n",d,"\n",ld[0][0:10],"\n",ld[2][0:10])
+#print(a[0][0:10],"\n",d,"\n",ld[0][0:10],"\n")
 dir_hom="data_homology"
 
 a_h,d_h=get_data_homology(arg,dir_hom,a_h,d_h)
 #print(a_h[0][0:10],"\n",d_h)
 
-x=input()
+n=2 #no. of numbers neighbors
+
+lsy,lcmap=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg)
+"""
+print(lsy,"\n",lcmap)
+lt=ldg[0]
+for x in lsy:
+
+    xr=lsy[x]['f']
+    xl=lsy[x]['b']
+    for g in range(len(xl)-1,-1,-1):
+        print(a[0].iloc[lt[xl[g]],[3,4]])
+    print("------------------\n",a[0].iloc[lt[x],[3,4]],"\n-------------------")
+    for g in xr:
+        print(a[0].iloc[lt[g],[3,4]])"""

process_data.py

@@ -1,6 +1,50 @@
 import pandas
 import gc
+import numpy as np
 
+def get_nearest_neighbors(g,gs,n,a,d,ld,ldg):
+    ne=[]
+    nr=[]
+    gi=d[gs.capitalize()]
+    sldf=a[gi]
+    sld=ld[gi]
+    sldg=ldg[gi]
+    if g not in sldg:
+        return ne
+    i=sldg[g]
+    #get the -n neighbors
+    start=int(sldf.iloc[i,[3]])
+    for j in range(n):
+        #select the column
+        itemp=0
+        end=sldf.iloc[:,4]
+        end=np.array(end)
+        assert(len(end)==len(sld))
+        end=end-start
+        end_s=np.argsort(end)
+        for k in end_s:
+            if end[k]<0 and end[k+1]>=0:
+                itemp=k
+                break
+        ne.append(sld[itemp])
+        start=int(sldf.iloc[itemp,[3]])
+        #print(start)
+    #get the +n neighbors
+    end=int(sldf.iloc[i,[4]])
+    for j in range(n):
+        itemp=0
+        start=sldf.iloc[:,3]
+        start=np.array(start)
+        start=start-end
+        start_s=np.argsort(start)
+        for k in start_s:
+            if start[k]>0:
+                itemp=k
+                break
+        nr.append(sld[itemp])
+        end=int(sldf.iloc[itemp,[4]])
+
+    return ne,nr
 
 ls=[]
 ld=[]
@@ -13,3 +57,27 @@ def list_dict_genomes(a,n):
         ls.append(uc)
         ld.append(ldg)
     return ls,ld
+
+def create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg):
+    lsy={} #dictionary which stores +/- n genes of the given gene by id. Each key is a gene id which corresponds to the one in center.
+    lcmap={} #dictionary which stores the gene pairs already considered
+    t=0
+    for df in a_h:
+        for index,row in df.iterrows():
+            x=row["gene_stable_id"]
+            y=row["homology_gene_stable_id"]
+            xs=row["species"]
+            ys=row["homology_species"]
+            if x+y in lcmap or y+x in lcmap:
+                continue
+            if x not in lsy:
+                xl,xr=get_nearest_neighbors(x,xs,n,a,d,ld,ldg)
+                lsy[x]=dict(b=xl,f=xr)
+            if y not in lsy:
+                yarr=[]
+                yl,yr=get_nearest_neighbors(y,ys,n,a,d,ld,ldg)
+                lsy[y]=dict(b=yl,f=yr)
+            lcmap[x+y]=1
+
+
+    return lsy,lcmap