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<p>Hi Jocelyn, </p>
<p>This is the example given in the Biopython tutorial, with just the id changed. If it is not returning the correct output (a seq_record with a sequence and sufficient features (around 1403)) then it is a Biopython issue.</p>
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<p>Downloading the entry as Genbank (full) allows it to be opened properly. It is therefore a tutorial issue as the commands given are not retrieving the record properly.</p>
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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="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Jocelyne <jocelyne@gmail.com><br>
<b>Sent:</b> 03 October 2017 19:57<br>
<b>To:</b> David Martin (Staff)<br>
<b>Cc:</b> biopython@lists.open-bio.org<br>
<b>Subject:</b> Re: [Biopython] Issues parsing genbank files</font>
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<div>Hi David:<br>
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I think if you are searching by id, you should only get 1 record. <br>
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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="LPlnk737534" previewremoved="true">https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/</a>
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<a id="LPUrlAnchor_15070576914600.06702893043400326" href="https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/" target="_blank" style="text-decoration: none;">MLA CE Course Manual: Molecular Biology Information ...</a></div>
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www.ncbi.nlm.nih.gov</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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<a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/" id="LPlnk640417" previewremoved="true">https://www.ncbi.nlm.nih.gov/books/NBK25501/</a><br>
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Jocelyne<br>
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<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>
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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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