<div dir="ltr"><div>Hi David:</div><div>If you are sure it's an issue, you should file an issue on the github project so that a contributor can take a look. Peter Cock is usually very responsive.<br></div><div><br></div><div></div><div>However, I submitted your query to entrez:</div><div><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=nc_003197&rettype=gb&retmode=text">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=nc_003197&rettype=gb&retmode=text</a></div><div>and attached the file I got.<br></div><div>I only got 1 feature.</div><div><br></div><div>I believe genes are in a different database (the 'gene' database) and you'll have to do the proper querying through eutils. <br></div><div><br></div><div>I'm not a developer on Biopython, and I didn't look into your issue closely so I could be wrong. Just trying to give you pointers.<br></div><div><br></div>Jocelyne<br><div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 3, 2017 at 12:12 PM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p>Hi Jocelyne,</p>
<p><br>
</p>
<p>Firstly apologies for missing the 'e' in your name before.</p>
<p><br>
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<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><span class="">
<p><br>
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<p>..d</p>
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<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>
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<div id="m_5877694653212212156divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><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>
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<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_5877694653212212156LPlnk289032" target="_blank">https://www.ncbi.nlm.nih.gov/<wbr>Class/MLACourse/Original8Hour/<wbr>Entrez/</a>
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<a id="m_5877694653212212156LPUrlAnchor_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>
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<a href="http://www.ncbi.nlm.nih.gov" target="_blank">www.ncbi.nlm.nih.gov</a></div>
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insert the description to be displayed by the search engine. Also searched by the search engine.</div>
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</span><a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/" id="m_5877694653212212156LPlnk495247" target="_blank">https://www.ncbi.nlm.nih.gov/<wbr>books/NBK25501/</a><br>
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Jocelyne<br>
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<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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<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>
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<p class="MsoNormal" style="line-height:15.0pt"><b><span style="font-size:10.5pt;color:#4365e2;letter-spacing:.9pt">Dr David M A Martin PhD FRSB</span></b><span style="font-size:10.0pt;color:#4365e2"><br>
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