Delete process_data.py

process_data.py

@@ -1,83 +0,0 @@
-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=[]
-def list_dict_genomes(a,n):
-    for x in a:
-        ldg={}
-        uc=list(x["gene_id"])
-        for i in range(len(uc)):
-            ldg[uc[i]]=i
-        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