<div dir="ltr">Many thanks <span style="font-size:11.9999990463257px">Thibaut</span><div><br></div><div>So... in regards to your question...</div><div><br></div><div>How can I query a specific clone and its correct coordinates if I know  the clone ID.</div><div><br></div><div>For example</div><div><br></div><div>assuming this clone:</div><div><span style="font-size:11.9999990463257px"> RP11-100N21</span><br></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px">In other words , how to I query the underlying clone dataset and output those clones in genomic coordinates?</span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px">Many thanks</span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px">Duarte</span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>     Duarte Miguel Paulo Molha      <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999">         <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>         <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 30 June 2015 at 13:15, Thibaut Hourlier <span dir="ltr"><<a href="mailto:thibaut@ebi.ac.uk" target="_blank">thibaut@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Duarte,<br>
The clone names are stored in the misc_* tables. So you need to use the MiscFeatureAdaptor, <a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1MiscFeatureAdaptor.html" rel="noreferrer" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1MiscFeatureAdaptor.html</a>:<br>
<br>
my $misc_clones = $mfa->fetch_all_by_Slice_and_set_code('tilepath');<br>
foreach my $clone (@$misc_clones) {<br>
 print join("\t", $clone->slice->seq_region_name, $clone->start, $clone->end, @{$clone->get_all_attribute_values('name')}), "\n";<br>
}<br>
<br>
A warning though, this is the tilepath so the boundaries of the clones are different from the contigs/clones in the assembly as sometimes they didn't use the entire clone for the assembly<br>
<br>
Hope this help<br>
<br>
Thibaut<br>
<div><div class="h5"><br>
> On 30 Jun 2015, at 11:50, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
><br>
> I used this code to get all the gebnomic coordinates of your subcontigs:<br>
><br>
><br>
> my @slices = @{ $slice_adaptor->fetch_all('clone') };<br>
> foreach my $slice (@slices){<br>
>       $progress->update();<br>
>       my $clone_name =  $slice->seq_region_name();<br>
>       my $projection = $slice->project('toplevel');<br>
>       foreach my $segment ( @{$projection} ) {<br>
>               my $to_slice = $segment->to_Slice();<br>
>               print join "\t", ("chr".$to_slice->seq_region_name(), $to_slice->start(), $to_slice->end(), $clone_name."\n");<br>
>       }<br>
> }<br>
><br>
> However, by doing this, the database does not fetch the original clone name<br>
><br>
> for example.. using this script I get<br>
> chr4    47567235        47733411        AC092597.1<br>
><br>
> However I would like to get :<br>
><br>
> chr4    47567235        47733411        RP11-100N21<br>
><br>
> Can someone explain what I am doing wrong?<br>
><br>
> Thanks<br>
><br>
> Duarte<br>
><br>
><br>
><br>
> =========================<br>
>      Duarte Miguel Paulo Molha<br>
>          <a href="http://about.me/duarte" rel="noreferrer" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
><br>
> On 30 June 2015 at 09:45, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
> Dear devs<br>
><br>
> How can I search for a specific clone id present on your tilepath<br>
><br>
> for example this: RP5-892C22<br>
><br>
> I would like to use the perl API if possible<br>
><br>
> Many thanks<br>
><br>
> Duarte<br>
><br>
><br>
><br>
> =========================<br>
>      Duarte Miguel Paulo Molha<br>
>          <a href="http://about.me/duarte" rel="noreferrer" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
><br>
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<br>
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</blockquote></div><br></div>