<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">My first question should have been which assembly are you using...<div class=""><br class=""></div><div class="">So yes this will work for GRCh37. Unfortunately it will not work for GRCh38 but this is something that we will fix for release 82.</div><div class=""><br class=""></div><div class="">So in the case of GRCh38, it is still possible but more complicated. It should work by getting the slice then projecting on the clone coordinate system</div><div class=""><br class=""></div><div class="">$subSlice = $misc_clone->feature_Slice;</div><div class="">$projectionSegment = $subSlice->project('clone')</div><div class=""><br class=""></div><div class="">Cheers</div><div class="">Thibaut</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 30 Jun 2015, at 13:56, Duarte Molha <<a href="mailto:duartemolha@gmail.com" class="">duartemolha@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Nevermind... after searching for miscFeatures information I found the relevant part in the api tutorial<div class=""><br class=""></div><div class="">Just for reference to anyone that has the same difficulties here is the relevant portion of the code I used:</div><div class="">(please let me know if there is something I did wrong Thibaut)</div><div class=""><br class=""></div><div class=""><div class="">my $mf_adaptor = $registry->get_adaptor( 'Human', 'Core', 'MiscFeature' );</div><div class=""><br class=""></div><div class="">open (IN, ,"<", $options->{list})|| die "Could not open ".$options->{list}." for reading \n";</div><div class="">my @input_queries = <IN>;</div><div class="">close IN;</div><div class=""><br class=""></div><div class="">foreach my $query (@input_queries){<br class=""></div><div class=""><span class="" style="white-space:pre"> </span>chomp $query;</div><div class=""><span class="" style="white-space:pre"> </span>my $clones = $mf_adaptor->fetch_all_by_attribute_type_value( 'clone_name', $query );<br class=""></div><div class=""><br class=""></div><div class=""><span class="" style="white-space:pre"> </span>while ( my $clone = shift @{$clones} ) {</div><div class=""><span class="" style="white-space:pre"> </span>my $slice = $clone->slice();</div><div class=""><span class="" style="white-space:pre"> </span>print join "\t", ("chr".$slice->seq_region_name(), $clone->start(), $clone->end() , $query."\n"); </div><div class=""><span class="" style="white-space:pre"> </span>}</div><div class="">}</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Best regards</div><div class=""><br class=""></div><div class="">Duarte</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999" class="">=========================<br class=""> Duarte Miguel Paulo Molha <br class=""></font><div class=""><font style="background-color:rgb(255,255,255)" color="#999999" class=""> <a href="http://about.me/duarte" target="_blank" class="">http://about.me/duarte</a> <br class="">=========================</font></div></div></div>
<br class=""><div class="gmail_quote">On 30 June 2015 at 13:26, Duarte Molha <span dir="ltr" class=""><<a href="mailto:duartemolha@gmail.com" target="_blank" class="">duartemolha@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Many thanks <span style="font-size:11.9999990463257px" class="">Thibaut</span><div class=""><br class=""></div><div class="">So... in regards to your question...</div><div class=""><br class=""></div><div class="">How can I query a specific clone and its correct coordinates if I know the clone ID.</div><div class=""><br class=""></div><div class="">For example</div><div class=""><br class=""></div><div class="">assuming this clone:</div><div class=""><span style="font-size:11.9999990463257px" class=""> RP11-100N21</span><br class=""></div><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><span style="font-size:11.9999990463257px" class="">In other words , how to I query the underlying clone dataset and output those clones in genomic coordinates?</span></div><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><span style="font-size:11.9999990463257px" class="">Many thanks</span></div><span class="HOEnZb"><font color="#888888" class=""><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><span style="font-size:11.9999990463257px" class="">Duarte</span></div><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><span style="font-size:11.9999990463257px" class=""><br class=""></span></div><div class=""><br class=""></div><div class=""><br class=""></div></font></span></div><div class="gmail_extra"><span class=""><br clear="all" class=""><div class=""><div class=""><font style="background-color:rgb(255,255,255)" color="#999999" class="">=========================<br class=""> Duarte Miguel Paulo Molha <br class=""></font><div class=""><font style="background-color:rgb(255,255,255)" color="#999999" class=""> <a href="http://about.me/duarte" target="_blank" class="">http://about.me/duarte</a> <br class="">=========================</font></div></div></div>
<br class=""></span><div class=""><div class="h5"><div class="gmail_quote">On 30 June 2015 at 13:15, Thibaut Hourlier <span dir="ltr" class=""><<a href="mailto:thibaut@ebi.ac.uk" target="_blank" class="">thibaut@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Duarte,<br class="">
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" class="">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1MiscFeatureAdaptor.html</a>:<br class="">
<br class="">
my $misc_clones = $mfa->fetch_all_by_Slice_and_set_code('tilepath');<br class="">
foreach my $clone (@$misc_clones) {<br class="">
print join("\t", $clone->slice->seq_region_name, $clone->start, $clone->end, @{$clone->get_all_attribute_values('name')}), "\n";<br class="">
}<br class="">
<br class="">
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 class="">
<br class="">
Hope this help<br class="">
<br class="">
Thibaut<br class="">
<div class=""><div class=""><br class="">
> On 30 Jun 2015, at 11:50, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank" class="">duartemolha@gmail.com</a>> wrote:<br class="">
><br class="">
> I used this code to get all the gebnomic coordinates of your subcontigs:<br class="">
><br class="">
><br class="">
> my @slices = @{ $slice_adaptor->fetch_all('clone') };<br class="">
> foreach my $slice (@slices){<br class="">
> $progress->update();<br class="">
> my $clone_name = $slice->seq_region_name();<br class="">
> my $projection = $slice->project('toplevel');<br class="">
> foreach my $segment ( @{$projection} ) {<br class="">
> my $to_slice = $segment->to_Slice();<br class="">
> print join "\t", ("chr".$to_slice->seq_region_name(), $to_slice->start(), $to_slice->end(), $clone_name."\n");<br class="">
> }<br class="">
> }<br class="">
><br class="">
> However, by doing this, the database does not fetch the original clone name<br class="">
><br class="">
> for example.. using this script I get<br class="">
> chr4 47567235 47733411 AC092597.1<br class="">
><br class="">
> However I would like to get :<br class="">
><br class="">
> chr4 47567235 47733411 RP11-100N21<br class="">
><br class="">
> Can someone explain what I am doing wrong?<br class="">
><br class="">
> Thanks<br class="">
><br class="">
> Duarte<br class="">
><br class="">
><br class="">
><br class="">
> =========================<br class="">
> Duarte Miguel Paulo Molha<br class="">
> <a href="http://about.me/duarte" rel="noreferrer" target="_blank" class="">http://about.me/duarte</a><br class="">
> =========================<br class="">
><br class="">
> On 30 June 2015 at 09:45, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank" class="">duartemolha@gmail.com</a>> wrote:<br class="">
> Dear devs<br class="">
><br class="">
> How can I search for a specific clone id present on your tilepath<br class="">
><br class="">
> for example this: RP5-892C22<br class="">
><br class="">
> I would like to use the perl API if possible<br class="">
><br class="">
> Many thanks<br class="">
><br class="">
> Duarte<br class="">
><br class="">
><br class="">
><br class="">
> =========================<br class="">
> Duarte Miguel Paulo Molha<br class="">
> <a href="http://about.me/duarte" rel="noreferrer" target="_blank" class="">http://about.me/duarte</a><br class="">
> =========================<br class="">
><br class="">
</div></div>> _______________________________________________<br class="">
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