<div style="font-family: 'Times New Roman'; font-size: 16px; "><div>Hi, Abu,</div><div><br /></div><div>I do not have your same Python and Biopython environments.</div><div><br /></div><div>But I have executed your same call to urllib with a slight modification to set the input argument as a string:</div><div><br /></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco"><span style="color: #0000ff">import</span> urllib</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Monaco; min-height: 15.0px"><span class="Apple-style-span" style="color: rgb(0, 170, 0); "><span style="color: #000000">f = urllib.urlopen(</span>'http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100'<span style="color: #000000">)</span></span></p></div><div><br /></div><div>And it was okay, only that you have received some typical HTML source code which you would have to parse it...</div><div><br /></div><div>Thanks,</div><div><br /></div><div>Angel Villahoz-Baleta</div><div>Bioinformatics Programmer</div><div>University of Wisconsin-Madison</div><div><br /></div><div><br /></div><div>On 02/23/10, <b class="name">Nizar Ghneim </b> <abumustafa3@gmail.com> wrote:</div><blockquote cite="mid: <27047_1266960992_ZZg0S4fs__ly6.00_f6ce41c51002231325p7e83a537y11bcd008fd5789ee@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid #00F; padding-left: 13px; margin-left: 0;" type="cite"><div class="mimepart text plain">Hello All,<br /><br />I have been using BioPython for a while now; this is my first time to post<br />on here. I currently have a list of ~150 miRNAs (that I obtained from a<br />microarray) that I would like analyze. My approach is to use TargetScan.org<br />(or miRanda, PicTar, etc.) to retrieve a list of target genes for each miRNA<br />in the list.<br /><br />Calling this website directly:<br />>><br /><a href="http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100" target="_blank">http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100</a><br />Will give me a list of gene targets for the miRNA hsa-mir-100<br /><br />Using the Bio.Entrez.efetch() method as I guide, I wrote the following code:<br /><br />import urllib<br />f = urllib.urlopen(<br /><a href="http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100" target="_blank">http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100</a><br />)<br /><br />I get the following error message:<br /><br /> File "c:\Python26\lib\urllib.py", line 87, in urlopen<br /> return opener.open(url)<br /> File "c:\Python26\lib\urllib.py", line 206, in open<br /> return getattr(self, name)(url)<br /> File "c:\Python26\lib\urllib.py", line 345, in open_http<br /> h.endheaders()<br /> File "c:\Python26\lib\httplib.py", line 892, in endheaders<br /> self._send_output()<br /> File "c:\Python26\lib\httplib.py", line 764, in _send_output<br /> self.send(msg)<br /> File "c:\Python26\lib\httplib.py", line 723, in send<br /> self.connect()<br /> File "c:\Python26\lib\httplib.py", line 704, in connect<br /> self.timeout)<br /> File "c:\Python26\lib\socket.py", line 514, in create_connection<br /> raise error, msg<br />IOError: [Errno socket error] [Errno 10061] No connection could be made<br />because the target machine actively refused it<br /><br />I have little to no experience with cgi (or any web-based programming for<br />that matter). Any help would be greatly appreciated.<br /><br />Thank you and regards,<br />Abu Mustafa<br />_______________________________________________<br />Biopython mailing list - Biopython@lists.open-bio.org<br /><a href="http://lists.open-bio.org/mailman/listinfo/biopython" target="_blank">http://lists.open-bio.org/mailman/listinfo/biopython</a><br /></div></blockquote></div>