Bioinformatics Programming
How to download files from an FTP server using Python?
In this article, we provide a simple Python script to download files from an FTP server using Python.
Write the FTP address and your username and password in the place specified below. Save this file in Python format (for example, download.py) and run it as:
$ python3 download.py
#!/usr/bin/env python3
import fnmatch
from ftplib import FTP
ftp = FTP('ftp address')
#if no username and password is required.
ftp.login()
#if username and password is required.
ftp.login('your-username','your-password')
# if you have to change directory on FTP server.
ftp.cwd('/path/to/dir/')
# Get all files
files = ftp.nlst()
# Download files
for file in files:
if fnmatch.fnmatch(file, '*.tar.gz'): #To download specific files.
print("Downloading..." + file)
try:
ftp.retrbinary("RETR " + file ,open("/path/to/dir/on/your/local/system/" + file, 'wb').write)
except EOFError: # To avoid EOF errors.
pass
ftp.close()
With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn. (more…)
Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding IDs. (more…)
Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)
You must be logged in to post a comment Login