import gzip

from ftplib import FTP

from io import StringIO

ftp = FTP('ftp.ncbi.nlm.nih.gov')

ftp.login()

r = StringIO()

ftp.retrbinary('RETR /pub/README_ABOUT_BZ2_FILES', r.write)

print r.getvalue()

#ftp://ftp.ncbi.nlm.nih.gov/pubmed/id_list.txt.gz

import ftputil

host = ftputil.FTPHost('ftp.ncbi.nlm.nih.gov', 'anonymous', '')

host.chdir('/pubmed/sample-2019-01-01/')

file_list = host.listdir(host.curdir)

#['example.xml', 'reflist.example.xml']

def read_file(fname):

with host.open(fname) as input_file:

for line in input_file:

yield line

for line in read_file("example.xml"):

print(line)

def read_gz_file(fname):

with host.open(fname, mode="rb") as input_file:

return gzip.GzipFile(fileobj=input_file)

host.chdir('/pubmed/')

i = 0

compressed_xml = read_gz_file("id_list.txt.gz")

for line in gzip.decompress(compressed_xml):

i += 1

print(i, line)

if i > 10:

break

print(i)

##----------------------------------------------------------------------------##

from ftplib import FTP

import gzip

from io import StringIO

ftp = FTP('ftp.ncbi.nlm.nih.gov')

ftp.login() # Username: anonymous password: anonymous@

sio = StringIO()

def handle_binary(more_data):

sio.write(more_data)

resp = ftp.retrbinary("RETR pub/pmc/PMC-ids.csv.gz", callback=handle_binary)

sio.seek(0) # Go back to the start

zippy = gzip.GzipFile(fileobj=sio)

uncompressed = zippy.read()

print(uncompressed[:1000])

import urllib

from io import BytesIO

import urllib.request

url = 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/id_list.txt.gz'

resp = urllib.request.urlopen(url)

memfile = BytesIO(resp.read())

with gzip.GzipFile(memfile, 'r') as myzip:

f = myzip.open('eggs.txt')

content = f.read() // or other file-like commands

zippy = gzip.GzipFile(fileobj=memfile)

uncompressed = zippy.read()

respData = resp.read()

#### !!!!

mysock = urllib.request.urlopen(url)

memfile = BytesIO(mysock.read())

f = gzip.GzipFile(fileobj=memfile)

r = f.read()

t = r.decode('utf-8')

###

import gzip

from io import BytesIO

import shutil

from ftplib import FTP

ftp = FTP('ftp.ncbi.nlm.nih.gov')

ftp.login('anonymous', '')

flo = BytesIO()

ftp.retrbinary('RETR /pubmed/id_list.txt.gz', flo.write)

flo.seek(0)

with open('archive.tar', 'wb') as fout, gzip.GzipFile(fileobj = flo) as gzip:

shutil.copyfileobj(gzip, fout)

with gzip.GzipFile(fileobj = flo) as gzip:

x = gzip.read()

gzipfile = gzip.GzipFile(mode='rb', fileobj=flo).read()

text = gzipfile.read()

buf = BytesIO(response.read())

f = gzip.GzipFile(fileobj=buf)

r = f.read()

###

import urllib

import io

from zipfile import ZipFile

mysock = urllib.urlopen('ftp://ftp.yourhost.com/spam.zip') # check urllib for parameters

memfile = io.BytesIO(mysock.read())

with ZipFile(memfile, 'r') as myzip:

f = myzip.open('eggs.txt')

content = f.read() // or other file-like commands