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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Many thanks. I’ll try that for my production code. As it is for student novices just getting in to biopython I’ll restructure the assignment
to read a genbank file they have downloaded instead of retrieving the entry from the DB.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">..d<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Leighton Pritchard [mailto:Leighton.Pritchard@hutton.ac.uk]
<br>
<b>Sent:</b> 02 November 2016 09:29<br>
<b>To:</b> David Martin (Staff) <d.m.a.martin@dundee.ac.uk><br>
<b>Cc:</b> biopython@lists.open-bio.org <biopython@mailman.open-bio.org><br>
<b>Subject:</b> Re: [Biopython] Errors with retrieval from Entrez<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi David,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">NCBI/Entrez queries are prone to this - I usually wrap the request in a structure that allows retries in case of errors, e.g. something like<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">```<o:p></o:p></p>
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<p class="MsoNormal"># Report last exception as string<br>
def last_exception():<br>
""" Returns last exception as a string, or use in logging."""<br>
exc_type, exc_value, exc_traceback = sys.exc_info()<br>
return ''.join(traceback.format_exception(exc_type, exc_value,<br>
exc_traceback))<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
# Retry Entrez requests (or any other function)<br>
def entrez_retry(fn, logger, *fnargs, **fnkwargs):<br>
"""Retries the passed function up to the number of times specified<br>
by args.retries<br>
"""<br>
tries, success = 0, False<br>
while not success and tries < args.retries:<br>
try:<br>
output = fn(*fnargs, **fnkwargs)<br>
success = True<br>
except:<br>
tries += 1<br>
logger.warning("Entrez query %s(%s, %s) failed (%d/%d)",<br>
fn, fnargs, fnkwargs, tries+1, args.retries)<br>
logger.warning(last_exception())<br>
if not success:<br>
logger.error("Too many Entrez failures (exiting)")<br>
sys.exit(1)<br>
return output<o:p></o:p></p>
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<p class="MsoNormal">```<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The except: clause would be better if it caught IncompleteRead…<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">L.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 2 Nov 2016, at 08:57, David Martin (Staff) <<a href="mailto:d.m.a.martin@dundee.ac.uk">d.m.a.martin@dundee.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I’m trying to retrieve a sequence from NCBI and am getting incomplete reads. Any hints or tips?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">..d<span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">handle= Entrez.efetch(db="nuccore", id=gi, retmode='text', rettype='gb')<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">seq= handle.read()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Traceback (most recent call last):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> File "<ipython-input-11-f879be0f80fe>", line 2, in <module><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> seq= handle.read()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> File "C:\Anaconda3\lib\http\client.py", line 440, in read<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> return self._readall_chunked()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> File "C:\Anaconda3\lib\http\client.py", line 550, in _readall_chunked<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> raise IncompleteRead(b''.join(value))<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">IncompleteRead: IncompleteRead(6841762 bytes read)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><br>
</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span class="apple-converted-space"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"> </span></span><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
Biopython mailing list - </span><a href="mailto:Biopython@mailman.open-bio.org"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#954F72">Biopython@mailman.open-bio.org</span></a><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><br>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Helvetica",sans-serif;color:black">--<br>
Dr Leighton Pritchard<br>
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme<br>
DG31, James Hutton Institute (Dundee)<br>
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA<br>
e: <a href="mailto:leighton.pritchard@hutton.ac.uk">leighton.pritchard@hutton.ac.uk</a> w:
<a href="http://www.hutton.ac.uk/staff/leighton-pritchard">http://www.hutton.ac.uk/staff/leighton-pritchard</a><br>
gpg/pgp: 0xFEFC205C tel: +44(0)844 928 5428 x8827 or +44(0)1382 568827<o:p></o:p></span></p>
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