ftpg.py

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.................")