<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">I’m trying to retrieve a sequence from NCBI and am getting incomplete reads. Any hints or tips?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">..d <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">handle= Entrez.efetch(db="nuccore", id=gi, retmode='text', rettype='gb')<o:p></o:p></p>
<p class="MsoNormal">seq= handle.read()<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Traceback (most recent call last):<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> File "<ipython-input-11-f879be0f80fe>", line 2, in <module><o:p></o:p></p>
<p class="MsoNormal"> seq= handle.read()<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> File "C:\Anaconda3\lib\http\client.py", line 440, in read<o:p></o:p></p>
<p class="MsoNormal"> return self._readall_chunked()<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> File "C:\Anaconda3\lib\http\client.py", line 550, in _readall_chunked<o:p></o:p></p>
<p class="MsoNormal"> raise IncompleteRead(b''.join(value))<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">IncompleteRead: IncompleteRead(6841762 bytes read)<o:p></o:p></p>
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>