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<p class="MsoNormal">Hello all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m looking for advice on how to handle Genbank records that reference other records as part of their location. My program iterates through large Genbank-formatted files with SeqIO.parse and extracts the CDS for subsequent analysis, using
feat.extract(). However, upon hitting a record where the feature location references another record, it SOMETIMES fails. For example,
<a href="http://www.ncbi.nlm.nih.gov/nuccore/DQ100169">http://www.ncbi.nlm.nih.gov/nuccore/DQ100169</a> seems to be handled correctly, while
<a href="http://www.ncbi.nlm.nih.gov/nuccore/DQ100170">http://www.ncbi.nlm.nih.gov/nuccore/DQ100170</a> gives a “ValueError: Feature references another sequence.” Curiously, in both cases the CDS feature itself doesn’t specify another record, only the parent
gene does.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My questions about this are:<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Why does the extraction fail on some records but not on all of them?<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Is there a way to extract the data I’m looking for without causing this error?<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">3)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>If the answer to (2) is no, is there some other way to check whether the sequence will cause this error, skip extracting that sequence, and exclude that record from the analysis?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for any help you can provide!<o:p></o:p></p>
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