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<p style="margin-top:0; margin-bottom:0">Dear seqinr users,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I'm trying to extract DNA sequences from GenBank using the "query" function from seqinr (I used to use it a lot a year ago and it was working well), but I got an erratic behaviour from the function reporting an error
message for a large number of species which have DNA sequences that I was able to get using the same function a year ago (sequences that can also be found through the NCBI web platform).</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Here an example with a problematic species (<span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">Pterois
antennata, taxonomic ID = <span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">185882) in the following web page <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882" class="OWAAutoLink" id="LPlnk796112" previewremoved="true">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882</a> we
can see the presence of 44 sequences in the Nucleotides database (sequences that I could get a year ago, using the same code).</span></span></p>
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<a id="LPUrlAnchor_15519320775450.8454946758073414" href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882" target="_blank" style="text-decoration:none">Taxonomy Browser</a></div>
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www.ncbi.nlm.nih.gov</div>
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THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.</div>
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Below the code I have used (I have tried on different computers but I'm getting the same results).
<p></p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">library(seqinr)</p>
<p style="margin-top:0; margin-bottom:0"><span>choosebank("genbank")</span><br>
</p>
<p style="margin-top:0; margin-bottom:0"><span><span>ee = seqinr::query("sp=Pterois antennata")</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span><span># the first time I got the following error message </span></span></p>
<p style="margin-top:0; margin-bottom:0"><span><span></p>
<div>Error in readLines(socket, n = nelem, ok = FALSE) : <br>
too few lines read in readLines<br>
<span><span></span></span><br>
<span><span></span></span></div>
</span></span>
<p></p>
<p style="margin-top:0; margin-bottom:0"><span><span># but trying again the same query I got the following error message:</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span><span><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">ee = seqinr::query("sp=Pterois
antennata")</span><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span><span></span></span></p>
<div>Error in seqinr::query("sp=Pterois antennata") : </div>
<div> invalid request:"FJ584021"</div>
<br>
<p></p>
<p style="margin-top:0; margin-bottom:0"># I also tried using the NCBI taxid</p>
<p style="margin-top:0; margin-bottom:0"></p>
<div><span>ee = seqinr::query("tid=185882")</span><br>
</div>
<span>Error in seqinr::query("tid=185882") : invalid request:"FJ584022"</span><br>
<p></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0">Interestingly the accession number reported in the error message for instance "<span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">FJ584022"
is a DNA sequences belonging to the species of interest "<span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">Pterois antennata"</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">I
don't really understand the problem considering that the function works for other species.</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">I'm
about to finalize a revision of a manuscript using this function as part of a new R package, and I would be really glad if you can find a solution to this problem!!!</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">Thanks
you very much in advance for your help greatly appreciated!</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">David
Eme</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">PS:
for information my sessionInfo() for the two computers i tried with are reported below.</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"></span></span></p>
<div>sessionInfo()</div>
<div>R version 3.4.4 (2018-03-15)</div>
<div>Platform: x86_64-pc-linux-gnu (64-bit)</div>
<div>Running under: Ubuntu 14.04.5 LTS</div>
<div><br>
</div>
<div>Matrix products: default</div>
<div>BLAS: /usr/lib/libblas/libblas.so.3.0</div>
<div>LAPACK: /usr/lib/lapack/liblapack.so.3.0</div>
<div><br>
</div>
<div>locale:</div>
<div> [1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C </div>
<div> [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8 </div>
<div> [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8 </div>
<div> [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C </div>
<div> [9] LC_ADDRESS=C LC_TELEPHONE=C </div>
<div>[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C </div>
<div><br>
</div>
<div>attached base packages:</div>
<div>[1] stats graphics grDevices utils datasets methods base </div>
<div><br>
</div>
<div>other attached packages:</div>
<div>[1] seqinr_3.4-5 regPhylo_1.0.1</div>
<div><br>
</div>
<div>loaded via a namespace (and not attached):</div>
<div>[1] MASS_7.3-44 compiler_3.4.4 tools_3.4.4 ade4_1.7-13 <br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><span>sessionInfo()</span><br>
</div>
<div>
<div>R version 3.5.2 (2018-12-20)<br>
Platform: x86_64-w64-mingw32/x64 (64-bit)<br>
Running under: Windows 10 x64 (build 17134)<br>
<br>
Matrix products: default<br>
<br>
locale:<br>
[1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New Zealand.1252 LC_MONETARY=English_New Zealand.1252<br>
[4] LC_NUMERIC=C LC_TIME=English_New Zealand.1252 <br>
<br>
attached base packages:<br>
[1] stats graphics grDevices utils datasets methods base <br>
<br>
other attached packages:<br>
[1] seqinr_3.4-5<br>
<br>
loaded via a namespace (and not attached):<br>
[1] MASS_7.3-51.1 compiler_3.5.2 ade4_1.7-13</div>
<br>
</div>
<div><br>
</div>
<br>
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<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
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