From e16611ba8181b2c2f8a0e5efdd52c374f8f0f234 Mon Sep 17 00:00:00 2001
From: HarshitGupta11 <50410275+HarshitGupta11@users.noreply.github.com>
Date: Mon, 12 Aug 2019 11:40:45 +0530
Subject: [PATCH] Add files via upload

---
 ftpg.py | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 ftpg.py

diff --git a/ftpg.py b/ftpg.py
new file mode 100644
index 0000000..f9334d1
--- /dev/null
+++ b/ftpg.py
@@ -0,0 +1,85 @@
+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")
+
+ch=input("Do you want to download the data?[y/n]")
+if ch=='y':
+    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.................")