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get_data.py

@@ -1,28 +1,50 @@
 import sys
 import os
-from req_data import get_data_file
-from read_data import read_data_genome
+from req_data import get_data_file,download_data
+from read_data import read_data_genome,read_data_homology
 from process_data import list_dict_genomes
 
-arg=sys.argv
-arg=arg[1:]
+def get_data_genome(arg,dir,a,d,ld,ldg):
+    if arg[0]=='-d':
+        if arg[4]=="-r":
+            c=0
+        else:
+            return a,d,ld,ldg
+    elif arg[0]=='-f':
+        get_data_file(arg[1],dir)
+    elif arg[0]=="-nd":
+        return ld,ldg,a,d
 
-a=[]
-d={}
+    if arg[4]=="-r":
+        a,d=read_data_genome(dir,a,d)
+        assert(len(a)==len(d))
 
-feature_name='gene'
+        ld,ldg=list_dict_genomes(a,d)
 
-if arg[0]=='-d':
-    a,d=read_data_genome(arg[1],a,d)
-elif arg[0]=='-f':
-    dir_name=get_data_file(arg[1])
-    a,d=read_data_genome(dir_name,a,d)
+        assert(len(ld)==len(ldg))
 
-assert(len(a)==len(d))
-
-ld,ldg=list_dict_genomes(a,d)
-
-assert(len(ld)==len(ldg))
-
-for i in range(len(ld)):
+        for i in range(len(ld)):
             assert(len(ld[i])==len(ldg[i]))
+
+    return ld,ldg,a,d
+
+def get_data_homology(arg,dir,a_h,d_h):
+    if arg[2]=="-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":
+            c=0
+        else:
+            return a_h,d_h
+    elif arg[2]=="-nd":
+        return a_h,d_h
+
+    if arg[4]=="-r":
+        a_h,d_h=read_data_homology(dir,a_h,d_h)
+        assert(len(a_h)==len(d_h))
+
+    return a_h,d_h

main.py

@@ -0,0 +1,27 @@
+import sys
+
+from get_data import get_data_homology,get_data_genome
+
+arg=sys.argv
+arg=arg[1:]
+
+if len(arg)!=5:
+    print("No. of arguments more or less. Please check")
+    sys.exit(1)
+
+a=[]
+d={}
+a_h=[]
+d_h={}
+ld=[]
+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])
+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()

my.txt

@@ -1,2 +1,3 @@
 ftp://ftp.ensembl.org/pub/release-96/gtf/lepisosteus_oculatus/Lepisosteus_oculatus.LepOcu1.96.gtf.gz
 ftp://ftp.ensembl.org/pub/release-96/gtf/mola_mola/Mola_mola.ASM169857v1.96.gtf.gz
+ftp://ftp.ensembl.org/pub/release-96/gtf/homo_sapiens/Homo_sapiens.GRCh38.96.gtf.gz

read_data.py

@@ -36,3 +36,15 @@ def read_data_genome(dir_name,a,dict_ind_genome):
         n=x.split(".")[0]
         dict_ind_genome[n]=len(a)-1
     return a,dict_ind_genome
+
+def read_data_homology(dir,a_h,d_h):
+    lf=os.listdir(dir)
+    if len(lf)==0:
+        print("No Files in the Directory!!!!!!!")
+        sys.exit(1)
+    for x in lf:
+        data=pd.read_csv(dir+"/"+x,compression='gzip',sep='\t')
+        a_h.append(data)
+        n=x.split(".")[0]
+        d_h[n]=len(a_h)-1
+    return a_h,d_h

req_data.py

@@ -7,10 +7,12 @@ import pandas as pd
 
 lf=[]
 
-dir_name="data"
+def download_data(x,dir_name):
+    fname=x.split("/")[-1]
+    path=os.path.join(dir_name,fname)
+    urllib.urlretrieve(x,path)
 
-def get_data_file(file):
-    print(file)
+def get_data_file(file,dir):
     if not os.path.isfile(file):
         print("The specified file does not exist!!!")
         sys.exit(1)
@@ -18,13 +20,7 @@ def get_data_file(file):
     with open(file,"r")as f:
         lf=f.read().splitlines()
 
-    if os.path.exists("data"):
-        print("Data Directory Already Exists!!!")
-
-    os.mkdir(dir_name)
+    if not os.path.exists(dir):
+        os.mkdir(dir)
     for x in lf:
-        fname=x.split("/")[-1]
-        path=os.path.join(dir_name,fname)
-        urllib.urlretrieve(x,path)
-
-    return dir_name
+        download_data(x,dir)