[Biopython] Retrieving miRNA target data from TargetScan

[Nizar Ghneim]

Hello All,

I have been using BioPython for a while now; this is my first time to post
on here. I currently have a list of ~150 miRNAs (that I obtained from a
microarray) that I would like analyze. My approach is to use TargetScan.org
(or miRanda, PicTar, etc.) to retrieve a list of target genes for each miRNA
in the list.

Calling this website directly:
>>
http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100
Will give me a list of gene targets for the miRNA hsa-mir-100

Using the Bio.Entrez.efetch() method as I guide, I wrote the following code:

import urllib
f = urllib.urlopen(
http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100
)

I get the following error message:

  File "c:\Python26\lib\urllib.py", line 87, in urlopen
    return opener.open(url)
  File "c:\Python26\lib\urllib.py", line 206, in open
    return getattr(self, name)(url)
  File "c:\Python26\lib\urllib.py", line 345, in open_http
    h.endheaders()
  File "c:\Python26\lib\httplib.py", line 892, in endheaders
    self._send_output()
  File "c:\Python26\lib\httplib.py", line 764, in _send_output
    self.send(msg)
  File "c:\Python26\lib\httplib.py", line 723, in send
    self.connect()
  File "c:\Python26\lib\httplib.py", line 704, in connect
    self.timeout)
  File "c:\Python26\lib\socket.py", line 514, in create_connection
    raise error, msg
IOError: [Errno socket error] [Errno 10061] No connection could be made
because the target machine actively refused it

I have little to no experience with cgi (or any web-based programming for
that matter). Any help would be greatly appreciated.

Thank you and regards,
Abu Mustafa