New folder download-data created

README.md

@@ -10,7 +10,7 @@ The aim of this project is to use **Deep Neural-Nets** to predict homology type
 The model uses a synteny matrix and some other factors derived from the species tree to make predictions. <br/>
 **Download The Required Files:**
 
-In order to download all the needed files run: `python ftpg.py`<br/>
+In order to download all the needed files run: `python download-data/ftpg.py`<br/>
 
 It will download the `gtf`, `cds` and `pep` files.
 

ftpg.py → download-data/ftpg.py

@@ -1,83 +1,83 @@
-from ftplib import FTP
-import progressbar
-import os
-import sys
-import urllib.request as urllib
-import requests
-
-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,dir):
-    if not os.path.isfile(file):
-        print("The specified file does not exist!!!")
-        sys.exit(1)
-
-    with open(file,"r")as f:
-        lf=f.read().splitlines()
-
-    if not os.path.exists(dir):
-        os.mkdir(dir)
-    for x in progressbar.progressbar(lf):
-        download_data(x,dir)
-
-
-
-#This wil download all the fasta files for the coding sequences. To change the directory, change the argument in the get_data_file argument.
-host ="ftp.ensembl.org"
-user = "anonymous"
-password = ""
-
-print("Connecting to {}".format(host))
-ftp = FTP(host)
-ftp.login(user, password)
-print("Connected to {}".format(host))
-base_link="ftp://ftp.ensembl.org"
-#find sequences of all the cds files
-l=ftp.nlst("/pub/release-96/fasta")
-lt=[]
-for x in l:
-    y=ftp.nlst(x+"/cds")
-    for z in y:
-        if z.endswith(".cds.all.fa.gz"):
-            lt.append(z)
-
-with open("seq_link.txt","w") as file:
-    for x in lt:
-        file.write(base_link+x)
-        file.write("\n")
-
-#find all the files with protein sequences
-l=ftp.nlst("/pub/release-96/fasta")
-lt=[]
-for x in progressbar.progressbar(l):
-    y=ftp.nlst(x+"/pep")
-    for z in y:
-        if z.endswith(".pep.all.fa.gz"):
-            lt.append(z)
-
-with open("protein_seq.txt","w") as file:
-    for x in lt:
-        file.write(base_link+x)
-        file.write("\n")
-#get link of all the gtf files
-l=ftp.nlst("/pub/release-96/gtf")
-lt=[]
-for x in l:
-    y=ftp.nlst(x)
-    for z in y:
-        if z.endswith(".96.gtf.gz"):
-            lt.append(z)
-
-with open("gtf_link.txt","w") as file:
-    for x in lt:
-        file.write(base_link+x)
-        file.write("\n")
-
-print("Downloading Data")
-get_data_file("gtf_link.txt","data")
-get_data_file("seq_link.txt","geneseq")
-get_data_file("protein_seq.txt","pro_seq")
-print("Download Complete.................")
+from ftplib import FTP
+import progressbar
+import os
+import sys
+import urllib.request as urllib
+import requests
+
+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,dir):
+    if not os.path.isfile(file):
+        print("The specified file does not exist!!!")
+        sys.exit(1)
+
+    with open(file,"r")as f:
+        lf=f.read().splitlines()
+
+    if not os.path.exists(dir):
+        os.mkdir(dir)
+    for x in progressbar.progressbar(lf):
+        download_data(x,dir)
+
+
+
+#This wil download all the fasta files for the coding sequences. To change the directory, change the argument in the get_data_file argument.
+host ="ftp.ensembl.org"
+user = "anonymous"
+password = ""
+
+print("Connecting to {}".format(host))
+ftp = FTP(host)
+ftp.login(user, password)
+print("Connected to {}".format(host))
+base_link="ftp://ftp.ensembl.org"
+#find sequences of all the cds files
+l=ftp.nlst("/pub/release-96/fasta")
+lt=[]
+for x in l:
+    y=ftp.nlst(x+"/cds")
+    for z in y:
+        if z.endswith(".cds.all.fa.gz"):
+            lt.append(z)
+
+with open("download-data/seq_link.txt","w") as file:
+    for x in lt:
+        file.write(base_link+x)
+        file.write("\n")
+
+#find all the files with protein sequences
+l=ftp.nlst("/pub/release-96/fasta")
+lt=[]
+for x in progressbar.progressbar(l):
+    y=ftp.nlst(x+"/pep")
+    for z in y:
+        if z.endswith(".pep.all.fa.gz"):
+            lt.append(z)
+
+with open("download-data/protein_seq.txt","w") as file:
+    for x in lt:
+        file.write(base_link+x)
+        file.write("\n")
+#get link of all the gtf files
+l=ftp.nlst("/pub/release-96/gtf")
+lt=[]
+for x in l:
+    y=ftp.nlst(x)
+    for z in y:
+        if z.endswith(".96.gtf.gz"):
+            lt.append(z)
+
+with open("download-data/gtf_link.txt","w") as file:
+    for x in lt:
+        file.write(base_link+x)
+        file.write("\n")
+
+print("Downloading Data")
+get_data_file("download-data/gtf_link.txt","data")
+get_data_file("download-data/seq_link.txt","geneseq")
+get_data_file("download-data/protein_seq.txt","pro_seq")
+print("Download Complete.................")