<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">Hello,<br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">I assume that the line  <br><div class="m_291851082605229685gmail-m_9114252400233638347gmail-lhs">Location   Chromosome 20: 3,208,063-3,219,836  reverse strand.</div><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">in [1] is the same as <br><br>my $slice = $slice_adaptor->fetch_by_regio<wbr>n( 'chromosome', '20' );<br>$sequence = $slice->subseq( 3208063, 3219836 );<br>print $sequence, "\n";<br><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">But the output of that script is not the same as the web page. I assume that 3208063 is  "relative to start of slice" according to the manual [2].<br><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">Any thought?<br></div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">The following code<br><pre class="m_291851082605229685gmail-code m_291851082605229685gmail-sh_perl m_291851082605229685gmail-sh_sourceCode"><span class="m_291851082605229685gmail-sh_keyword">my</span> <span class="m_291851082605229685gmail-sh_variable">$coord_sys</span>  <span class="m_291851082605229685gmail-sh_symbol">=</span> <span class="m_291851082605229685gmail-sh_variable">$slice</span><span class="m_291851082605229685gmail-sh_symbol">-></span><span class="m_291851082605229685gmail-sh_function">coord_system</span><span class="m_291851082605229685gmail-sh_symbol">()-></span><span class="m_291851082605229685gmail-sh_function">name</span><span class="m_291851082605229685gmail-sh_symbol">()<wbr>;</span>
<span class="m_291851082605229685gmail-sh_keyword">my</span> <span class="m_291851082605229685gmail-sh_variable">$seq_region</span> <span class="m_291851082605229685gmail-sh_symbol">=</span> <span class="m_291851082605229685gmail-sh_variable">$slice</span><span class="m_291851082605229685gmail-sh_symbol">-></span><span class="m_291851082605229685gmail-sh_function">seq_region_name</span><span class="m_291851082605229685gmail-sh_symbol">();</span>
<span class="m_291851082605229685gmail-sh_keyword">my</span> <span class="m_291851082605229685gmail-sh_variable">$start</span>      <span class="m_291851082605229685gmail-sh_symbol">=</span> <span class="m_291851082605229685gmail-sh_variable">$slice</span><span class="m_291851082605229685gmail-sh_symbol">-></span><span class="m_291851082605229685gmail-sh_function">start</span><span class="m_291851082605229685gmail-sh_symbol">();</span>
<span class="m_291851082605229685gmail-sh_keyword">my</span> <span class="m_291851082605229685gmail-sh_variable">$end</span>        <span class="m_291851082605229685gmail-sh_symbol">=</span> <span class="m_291851082605229685gmail-sh_variable">$slice</span><span class="m_291851082605229685gmail-sh_symbol">-></span><span class="m_291851082605229685gmail-sh_function">end</span><span class="m_291851082605229685gmail-sh_symbol">();</span>
<span class="m_291851082605229685gmail-sh_keyword">my</span> <span class="m_291851082605229685gmail-sh_variable">$strand</span>     <span class="m_291851082605229685gmail-sh_symbol">=</span> <span class="m_291851082605229685gmail-sh_variable">$slice</span><span class="m_291851082605229685gmail-sh_symbol">-></span><span class="m_291851082605229685gmail-sh_function">strand</span><span class="m_291851082605229685gmail-sh_symbol">();</span>

<span class="m_291851082605229685gmail-sh_keyword">print</span> <span class="m_291851082605229685gmail-sh_string">"Slice: $coord_sys $seq_region $start-$end ($strand)\n"</span><span class="m_291851082605229685gmail-sh_symbol">;</span></pre><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">returns<br>Slice: chromosome 20 1-63025520 (1)<br><br><br><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">If I use <br>my $slice = $slice_adaptor->fetch_by_gene_<wbr>stable_id( 'ENSG00000088836' );<br><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">I get<br>Slice: chromosome 20 3208063-3219836 (1)<br><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">which is correct.<br></div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br>[1] <a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000088836;r=20:3208063-3219836" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Gene/Sequence?db=core<wbr>;g=ENSG00000088836;r=20:320806<wbr>3-3219836</a><br>[2] <a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Slice.html#a32e3dc700dc76a7b7450f3664de47d5f" target="_blank">http://www.ensembl.org/info/do<wbr>cs/Doxygen/core-api/classBio_<wbr>1_1EnsEMBL_1_1Slice.html#a32e3<wbr>dc700dc76a7b7450f3664de47d5f</a><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br clear="all"></div><div><div class="m_291851082605229685gmail-m_9114252400233638347gmail_signature"><div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>Mahmood</font><br><br><br></div></div></div>
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