<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:0px 0px 1.2em!important">Hi David,</p>
<p style="margin:0px 0px 1.2em!important">Unfortunately, it is an Entrez question rather than a biopython question. I feel your pain, but blame NCBI for their often confusing choices and poor documentation. </p>
<p style="margin:0px 0px 1.2em!important">Check <a href="https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly">out this</a>… What you want I think is <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline">db="nuccore"</code> and <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline">rettype="gbwithparts"</code>:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code class="hljs language-python" style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline;white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;overflow-x:auto;padding:0.5em;color:rgb(51,51,51);background:rgb(248,248,248)">> <span class="hljs-keyword" style="color:rgb(51,51,51);font-weight:bold">with</span> Entrez.efetch(db=<span class="hljs-string" style="color:rgb(221,17,68)">"nuccore"</span>, rettype=<span class="hljs-string" style="color:rgb(221,17,68)">"gbwithparts"</span>, retmode=<span class="hljs-string" style="color:rgb(221,17,68)">"text"</span>, id=<span class="hljs-string" style="color:rgb(221,17,68)">"NC_003197"</span>) <span class="hljs-keyword" style="color:rgb(51,51,51);font-weight:bold">as</span> handle:
> seq_record = SeqIO.read(handle, <span class="hljs-string" style="color:rgb(221,17,68)">"gb"</span>) <span class="hljs-comment" style="color:rgb(153,153,136);font-style:italic">#using "gb" as an alias for "genbank"</span>
> print(<span class="hljs-string" style="color:rgb(221,17,68)">"%s with %i features"</span> % (<a href="http://seq_record.id">seq_record.id</a>, len(seq_record.features)))
NC_003197<span class="hljs-number" style="color:rgb(0,128,128)">.2</span> <span class="hljs-keyword" style="color:rgb(51,51,51);font-weight:bold">with</span> <span class="hljs-number" style="color:rgb(0,128,128)">14045</span> features
</code></pre>
<p style="margin:0px 0px 1.2em!important">Cheers!<br>Kevin</p>
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bjwvc3Bhbj48L3A+PC9kaXY+" style="height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0em;padding:0;margin:0"></div></div><div><p class="m_8441605794541111680gmail-p1"><span class="m_8441605794541111680gmail-s1"></span></p></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Oct 3, 2017 at 4:30 PM David Martin (Staff) <<a href="mailto:d.m.a.martin@dundee.ac.uk" target="_blank">d.m.a.martin@dundee.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr">
<p>Hi Jocelyne,</p>
<p><br>
</p>
<p>Firstly apologies for missing the 'e' in your name before.</p>
<p><br>
</p>
<p>The record being retrieved is a single sequence record - it is a bacterial chromosome. It should have many features, most corresponding to genes encoded within the chromosome. </p></div></div><div dir="ltr"><div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr">
<p><br>
</p>
<p>..d</p>
<p><br>
</p>
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670Signature">
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<div name="divtagdefaultwrapper">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">Dr David Martin<br>
Senior Lecturer in Bioinformatics<br>
College of Life Sciences<br>
University of Dundee<br>
<br>
</div>
</div>
</div>
</div>
</div>
<br>
<br>
</div></div><div dir="ltr"><div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr"><div style="color:rgb(0,0,0)">
<hr style="display:inline-block;width:98%">
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Jocelyne <<a href="mailto:jocelyne@gmail.com" target="_blank">jocelyne@gmail.com</a>><br>
<b>Sent:</b> 03 October 2017 19:57<br>
<b>To:</b> David Martin (Staff)<br>
<b>Cc:</b> <a href="mailto:biopython@lists.open-bio.org" target="_blank">biopython@lists.open-bio.org</a><br>
<b>Subject:</b> Re: [Biopython] Issues parsing genbank files</font>
<div> </div>
</div>
</div></div></div><div dir="ltr"><div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr"><div style="color:rgb(0,0,0)"><div><div dir="ltr"><div>
<div>
<div>Hi David:<br>
</div>
I think if you are searching by id, you should only get 1 record. <br>
</div>
The questions you are asking sound to me like Entrez / NCBI databases questions, not necessarily Biopython questions. Unless someone else has time to dive into your specific example, I suggest you look at this documentation:<br>
<a href="https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/" id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPlnk289032" target="_blank">https://www.ncbi.nlm.nih.gov/C<wbr>lass/MLACourse/Original8Hour/E<wbr>ntrez/</a>
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPBorder_GT_15070578530400.6585899649075668" style="margin-bottom:20px;overflow:auto;width:100%;text-indent:0px">
<table id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPContainer_15070578530320.37270568043257524" cellspacing="0" style="width:90%;background-color:rgb(255,255,255);overflow:auto;padding-top:20px;padding-bottom:20px;margin-top:20px;border-top:1px dotted rgb(200,200,200);border-bottom:1px dotted rgb(200,200,200)">
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<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPRemovePreviewContainer_15070578530350.24206507103057295"></div>
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPTitle_15070578530350.39796956705483066" style="color:rgb(0,120,215);font-weight:normal;font-size:21px;font-family:wf_segoe-ui_light,"Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;line-height:21px">
<a id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPUrlAnchor_15070578530370.5661820631142123" href="https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/" style="text-decoration:none" target="_blank">MLA CE Course Manual: Molecular Biology Information ...</a></div>
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPMetadata_15070578530370.1967457617256929" style="margin:10px 0px 16px;color:rgb(102,102,102);font-weight:normal;font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:14px;line-height:14px">
<a href="http://www.ncbi.nlm.nih.gov" target="_blank">www.ncbi.nlm.nih.gov</a></div>
<div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPDescription_15070578530380.7769491901733283" style="display:block;color:rgb(102,102,102);font-weight:normal;font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:14px;line-height:20px;max-height:100px;overflow:hidden">
insert the description to be displayed by the search engine. Also searched by the search engine.</div>
</td>
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</div>
<br>
<br>
</div></div></div></div></div></div><div dir="ltr"><div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr"><div style="color:rgb(0,0,0)"><div><div dir="ltr"><div><a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/" id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670LPlnk495247" target="_blank">https://www.ncbi.nlm.nih.gov/b<wbr>ooks/NBK25501/</a><br>
</div>
Jocelyne<br>
<div>
<div>
<div> <br>
<br>
<br>
<br>
</div>
</div>
</div>
</div></div></div></div></div><div dir="ltr"><div id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr"><div style="color:rgb(0,0,0)"><div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Oct 3, 2017 at 2:39 AM, David Martin (Staff) <span dir="ltr">
<<a href="mailto:d.m.a.martin@dundee.ac.uk" target="_blank">d.m.a.martin@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-GB">
<div class="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555WordSection1">
<p class="MsoNormal">Hi folks,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I’m trying to parse some bacterial genomes. I’ve lifted the following code from the biopython tutorial but it seems to be giving issues.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-family:Consolas">from Bio import Entrez<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">from Bio import SeqIO<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">Entrez.email = "<a href="mailto:A.N.Other@example.com" target="_blank">A.N.Other@example.com</a>"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id="nc_003197") as handle:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas"> seq_record = SeqIO.read(handle, "gb") #using "gb" as an alias for "genbank"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">print("%s with %i features" % (<a href="http://seq_record.id" target="_blank">seq_record.id</a>, len(seq_record.features)))<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I get one feature instead of the thousands expected.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Trying to extract a single gene I get a run of NN instead of sequence.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thoughts: This is initially retrieved as a set of annotations but no sequence. Is there a way to ensure entrez retrieves the full data?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">..d<u></u><u></u></p>
<p class="MsoNormal"><a href="//sig/" target="_blank"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1032" alt="Email signature" width="1" height="2" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/emailsignature/tiny.png"></span></a><span style="font-size:12pt;font-family:"Times New Roman",serif"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman",serif"> <u></u><u></u></span></p>
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<p class="MsoNormal"><a href="http://uod.ac.uk/sig-home" target="_blank"><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1031" alt="University of Dundee shield logo" width="73" height="73" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/university-of-dundee-email-favicon.png"></span></a><span style="font-size:7.5pt;font-family:"Times New Roman",serif"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman",serif"> <u></u><u></u></span></p>
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<p class="MsoNormal" style="line-height:15pt"><b><span style="font-size:10.5pt;color:rgb(67,101,226);letter-spacing:0.9pt">Dr David M A Martin PhD FRSB</span></b><span style="font-size:10pt;color:rgb(67,101,226)"><br>
Senior Lecturer in Bioinformatics<br>
School of Life Sciences, University of Dundee<br>
<a href="tel:+44%201382%20388704" value="+441382388704" target="_blank">+44(0)1382 388704</a> |
<a href="mailto:d.m.a.martin@dundee.ac.uk@dundee.ac.uk" target="_blank"><span style="color:rgb(67,101,226);text-decoration:none">d.m.a.martin@dundee.ac.uk</span></a><u></u><u></u></span></p>
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<p class="MsoNormal"><a href="http://uod.ac.uk/sig-fb" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1030" alt="University of Dundee Facebook" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-facebook.png"></span></a><a href="http://uod.ac.uk/sig-tw" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1029" alt="University of Dundee Twitter" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-twitter.png"></span></a><a href="http://uod.ac.uk/sig-li" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1028" alt="University of Dundee LinkedIn" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-linkedin.png"></span></a><a href="http://uod.ac.uk/sig-yt" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1027" alt="University of Dundee YouTube" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-youtube.png"></span></a><a href="http://uod.ac.uk/sig-ig" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1026" alt="University of Dundee Instagram" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-instagram.png"></span></a><a href="http://uod.ac.uk/sig-sc" target="_blank"><span style="font-size:9pt;color:blue;text-decoration:none"><img id="m_8441605794541111680gmail-m_-2656298781514942350m_9081958797916729670m_3041449790183323555_x0000_i1025" alt="University of Dundee Snapchat" width="32" height="32" border="0" src="https://www.dundee.ac.uk/media/dundeewebsite/themes/brandnewhope/img/baxter-blue-snapchat.png"></span></a><span style="font-size:9pt;color:rgb(67,101,226)"> </span><span style="font-size:12pt;font-family:"Times New Roman",serif"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;color:rgb(136,136,136)"><a href="http://uod.ac.uk/sig-strapline" target="_blank"><b><span style="color:rgb(67,101,226);text-decoration:none">We're Scottish University of the Year again!</span></b></a><br>
The Times / Sunday Times Good University Guide 2016 and 2017</span><span style="font-size:12pt;font-family:"Times New Roman",serif"><u></u><u></u></span></p>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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