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<div style="color: rgb(0, 0, 0); font-size: 14px; ">Thanks Magali,</div>
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<div style="color: rgb(0, 0, 0); font-size: 14px; ">If that is the case I will just get the chromosomes and query locally. Could I suggest that the API documentation is updated to reflect this/make it clearer? I.e. In "fetch_<span style="font-style: italic; ">by_</span>region"
it appears that sequences can be downloaded specific to a coordinate system by including the version of the coordinate system.</div>
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<div style="color: rgb(0, 0, 0); font-size: 14px; ">Ash</div>
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<span style="font-weight:bold">From: </span>mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 21 August 2014 6:14 PM<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] getting sequences from older assemblies using the Perl API<br>
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<div bgcolor="#FFFFFF" text="#000000">Hi Ash,<br>
<br>
We do not store dna sequences other than those for the latest available assembly version.<br>
<br>
We provide some mappings between chromosomes in previous versions and the chromosomes from the latest version.<br>
This allows you to map features between assemblies, but not access the dna sequence.<br>
<br>
If you need the dna sequence for those assemblies, I would recommend using the archived version where that assembly was the primary assembly.<br>
For mouse NCBIm37, this would be release 67:<br>
<a class="moz-txt-link-freetext" href="http://may2012.archive.ensembl.org/Mus_musculus/Info/Index">http://may2012.archive.ensembl.org/Mus_musculus/Info/Index</a><br>
<br>
For human GRCh37, this was in release 75:<br>
<a class="moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Info/Index">http://grch37.ensembl.org/Homo_sapiens/Info/Index</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 21/08/2014 07:13, Ashley Waardenberg wrote:<br>
</div>
<blockquote cite="mid:D01BCAF7.2605C%25A.waardenberg@victorchang.edu.au" type="cite">
<div style="color: rgb(0, 0, 0); ">
<div>
<div>If I select any other assembly version (below as variable "$version") other than the highest ranked, I seem to only get "N" as sequences returned. I have tried this for both mouse and human. This is using the perl API version 75, below is an example querying
a sequence at some specific coordinate. If I retrieve the soft-masked region, it returns lower cases where expected, but is still all "n". If I change the assembly to highest rank (e.g. GRCm38) it retrieves "proper" sequence, but obviously at the wrong coordinates
as I am using NCBIM37 fragments.</div>
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<div style="color: rgb(0, 0, 0); "><br>
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<div style="color: rgb(0, 0, 0); ">Is this a possible bug/any ideas?</div>
<div style="color: rgb(0, 0, 0); "><br>
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<div style="color: rgb(0, 0, 0); ">Ash</div>
<div style="color: rgb(0, 0, 0); "><br>
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<div style="color: rgb(0, 0, 0); ">#code start</div>
<div>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">use</span> Bio::EnsEMBL::Registry;</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<span class="Apple-style-span" style="color: rgb(212, 39, 34);
"><span style="color: #be299d"><br>
</span></span></p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<span class="Apple-style-span" style="color: rgb(212, 39, 34);
"><span style="color: #be299d">my</span><span style="color:
#000000"> $registry =
</span>"Bio::EnsEMBL::Registry"<span style="color: #000000">;</span></span></p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $species = <span style="color: #d42722">"mouse"</span>;</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $version = <span style="color: #d42722">"NCBIM37"</span>;</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<br>
</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
$registry->load_registry_from_db( </p>
<p style="margin-top: 0px; margin-right: 0px; margin-bottom:
0px; margin-left: 0px; font: normal normal normal 11px/normal
Menlo; color: rgb(212, 39, 34); ">
<span style="color: #000000"> -host => </span>'ensembldb.ensembl.org'<span style="color: #000000">, </span></p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
-user => <span style="color: #d42722">'anonymous'</span> </p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
);</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<br>
</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $adaptor = $registry->get_adaptor($species,<span style="color:
#d42722">'Core'</span>,<span style="color: #d42722">'Slice'</span>);</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<span class="Apple-style-span" style="color: rgb(0, 132, 35);
">#slice of interest:</span></p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $slice = $adaptor->fetch_by_region(<span style="color: #d42722">'chromosome'</span>,
<span style="color: #2f2fd1">7</span> , <span style="color:
#2f2fd1">
123336212</span> , <span style="color: #2f2fd1">123338053</span> , <span style="color: #2f2fd1">
1</span>, $version);</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<span class="Apple-style-span" style="color: rgb(0, 132, 35);
">#different elements of the slice:</span></p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $sequence = $slice->seq();</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<span style="color: #be299d">my</span> $softmasked = $slice->get_repeatmasked_seq(
<span style="color: #be299d">undef</span>, <span style="color: #2f2fd1">1</span> );</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">my</span> $softmasked_seq = $softmasked->seq();</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; min-height: 13px; ">
<br>
</p>
<p style="margin-top: 0px; margin-right: 0px; margin-bottom:
0px; margin-left: 0px; font: normal normal normal 11px/normal
Menlo; color: rgb(0, 132, 35); ">
#print sliced sequences:</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">print</span> $sequence.<span style="color: #d42722">"\n"</span>.<span style="color:
#d42722">"\n"</span>.<span style="color: #d42722">"\n"</span>;</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span style="color: #be299d">print</span> $softmasked_seq.<span style="color: #d42722">"\n"</span>;</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<span class="Apple-style-span" style="font-size: 14px; font-family: Calibri, sans-serif; "></span></p>
<div>#code end</div>
<div><br>
</div>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
#this prints the following out:</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
<br>
</p>
<p style="color: rgb(0, 0, 0); margin-top: 0px; margin-right:
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal
normal 11px/normal Menlo; ">
</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><br>
</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><br>
</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN</p>
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