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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 am new to seqinr. Today I was trying to connect to the genbank database and send queries. It worked well for some sequences:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">> choosebank("genbank")<o:p></o:p></p>
<p class="MsoNormal">> query("lambda","AC=CP001252")<o:p></o:p></p>
<p class="MsoNormal">> mylambda <- get("lambda",env=.seqinrEnv)<o:p></o:p></p>
<p class="MsoNormal">> attributes(mylambda)<o:p></o:p></p>
<p class="MsoNormal">$names<o:p></o:p></p>
<p class="MsoNormal">[1] "call" "name" "nelem" "typelist" "req" "socket"
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">$class<o:p></o:p></p>
<p class="MsoNormal">[1] "qaw"<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However, for a set of other sequences an error was thrown:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">> query("dengue1", "AC=NC001477")<o:p></o:p></p>
<p class="MsoNormal">Error in query("dengue1", "AC=NC001477") : <o:p></o:p></p>
<p class="MsoNormal"> invalid request:"unknown accession number at (^): \"AC<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And not only accession number, using other parameters also incurs error:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">> query('naturepaper', 'R=Nature/460/352')<o:p></o:p></p>
<p class="MsoNormal">Error in query("naturepaper", "R=Nature/460/352") : <o:p></o:p></p>
<p class="MsoNormal"> invalid request:"unknown reference at (^): \"R<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In addition, I also found that not all databases could be loaded:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">> choosebank("refseqViruses")<o:p></o:p></p>
<p class="MsoNormal">Error in acnucopen(bank, socket) : <o:p></o:p></p>
<p class="MsoNormal"> Database with name -->refseqViruses<-- is not known by server.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Could anyone let me know how should I fix these problems? Version of this seqinr package is 3.3-6, running under 64-bit R in Win10 system.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you and best regards,<o:p></o:p></p>
<p class="MsoNormal">Ran Wei <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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