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<p class="MsoNormal">Hi folks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:Consolas">from Bio import Entrez<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">from Bio import SeqIO<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">Entrez.email = "A.N.Other@example.com"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id="nc_003197") as handle:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Consolas"> seq_record = SeqIO.read(handle, "gb") #using "gb" as an alias for "genbank"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">print("%s with %i features" % (seq_record.id, len(seq_record.features)))<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I get one feature instead of the thousands expected.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Trying to extract a single gene I get a run of NN instead of sequence.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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?<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"><a href="//sig/"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:blue;mso-fareast-language:EN-GB;text-decoration:none"><img border="0" width="1" height="2" id="_x0000_i1032" src="https://www.dundee.ac.uk/media/dundeewebsite/emailsignature/tiny.png" alt="Email signature"></span></a><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<b><span style="font-size:10.5pt;color:#4365E2;letter-spacing:.9pt;mso-fareast-language:EN-GB">Dr David M A Martin PhD FRSB</span></b><span style="font-size:10.0pt;color:#4365E2;mso-fareast-language:EN-GB"><br>
Senior Lecturer in Bioinformatics<br>
School of Life Sciences, University of Dundee<br>
+44(0)1382 388704 | <a href="mailto:d.m.a.martin@dundee.ac.uk@dundee.ac.uk"><span style="color:#4365E2;text-decoration:none">d.m.a.martin@dundee.ac.uk</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;color:#888888;mso-fareast-language:EN-GB"><a href="http://uod.ac.uk/sig-strapline"><b><span style="color:#4365E2;text-decoration:none">We're Scottish University of the Year again!</span></b></a><br>
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