<p dir="ltr">I would still appreciate some help with this query. If possible.</p>
<div class="gmail_quote">On 30 Jun 2015 16:29, "Duarte Molha" <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thibaut... Could you expand on how I can change my script to make it work with the new assembly?</div><div>I have just realised that the reason I am no getting 60 BAC entries is because their are only present in GRCh38 and not on the GRCh37</div><div><br></div><div>Can you tell me how I can modify my script to work with the new assembly?</div><div><br></div><div>I don't seem to understand the projection method you are using.<br></div><div>Here is the relevant part of my script </div><div><br></div><div>my $mf_adaptor = $registry->get_adaptor( 'Human', 'Core', 'MiscFeature' );</div><div><br></div><div>open (IN, ,"<", $options->{list})|| die "Could not open ".$options->{list}." for reading \n";</div><div>my @input_queries = <IN>;</div><div>close IN;</div><div><br></div><div>foreach my $query (@input_queries){</div><div><span style="white-space:pre-wrap"> </span>chomp $query;</div><div><span style="white-space:pre-wrap"> </span>my $clones = $mf_adaptor->fetch_all_by_attribute_type_value( 'clone_name', $query );</div><div><br></div><div><span style="white-space:pre-wrap"> </span>while ( my $clone = shift @{$clones} ) {</div><div><span style="white-space:pre-wrap"> </span>my $slice = $clone->slice();</div><div><span style="white-space:pre-wrap"> </span>print join "\t", ("chr".$slice->seq_region_name(), $clone->start(), $clone->end() , $query."\n"); </div><div><span style="white-space:pre-wrap"> </span>}</div><div>}</div><div><br></div><div><br></div><div>Best regards</div><div><br></div><div>Duarte</div></div><div class="gmail_extra"><br clear="all"><div><div><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 15:46, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">no. That does not get anything.<div><br></div><div><br></div></div><div class="gmail_extra"><span><br clear="all"><div><div><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></span><div><div><div class="gmail_quote">On 30 June 2015 at 14:50, 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"><div style="word-wrap:break-word">If you use name instead of clone_name, does it fetches the missing one?<div><br></div><div>Cheers</div><span><font color="#888888"><div>Thibaut</div></font></span><div><div><div><br><div><blockquote type="cite"><div>On 30 Jun 2015, at 14:27, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Yes I am using the GRCh37 Thibaut ... so I am ok for now... but it is good to know this does not work with the latest assembly. <div>However... can you please answer my question regarding the missing clones like <span style="font-size:11.9999990463257px"> </span><span style="font-size:11.9999990463257px">RP11-155D3 ... why can I not fetch this when it is clearly on the database?</span></div><div><span style="font-size:11.9999990463257px"><br></span></div><div><span style="font-size:11.9999990463257px">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><b><br></b></div></div><div class="gmail_extra"><br clear="all"><div><div><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 14:12, 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"><div style="word-wrap:break-word">My first question should have been which assembly are you using...<div><br></div><div>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><br></div><div>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><br></div><div>$subSlice = $misc_clone->feature_Slice;</div><div>$projectionSegment = $subSlice->project('clone')</div><div><br></div><div>Cheers</div><span><font color="#888888"><div>Thibaut</div></font></span><div><div><div><br><div><blockquote type="cite"><div>On 30 Jun 2015, at 13:56, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Nevermind... after searching for miscFeatures information I found the relevant part in the api tutorial<div><br></div><div>Just for reference to anyone that has the same difficulties here is the relevant portion of the code I used:</div><div>(please let me know if there is something I did wrong Thibaut)</div><div><br></div><div><div>my $mf_adaptor = $registry->get_adaptor( 'Human', 'Core', 'MiscFeature' );</div><div><br></div><div>open (IN, ,"<", $options->{list})|| die "Could not open ".$options->{list}." for reading \n";</div><div>my @input_queries = <IN>;</div><div>close IN;</div><div><br></div><div>foreach my $query (@input_queries){<br></div><div><span style="white-space:pre-wrap"> </span>chomp $query;</div><div><span style="white-space:pre-wrap"> </span>my $clones = $mf_adaptor->fetch_all_by_attribute_type_value( 'clone_name', $query );<br></div><div><br></div><div><span style="white-space:pre-wrap"> </span>while ( my $clone = shift @{$clones} ) {</div><div><span style="white-space:pre-wrap"> </span>my $slice = $clone->slice();</div><div><span style="white-space:pre-wrap"> </span>print join "\t", ("chr".$slice->seq_region_name(), $clone->start(), $clone->end() , $query."\n"); </div><div><span style="white-space:pre-wrap"> </span>}</div><div>}</div></div><div><br></div><div><br></div><div>Best regards</div><div><br></div><div>Duarte</div></div><div class="gmail_extra"><br clear="all"><div><div><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 13:26, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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><span><font color="#888888"><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></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div><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></span><div><div><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><br>
> On 30 Jun 2015, at 11:50, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">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" target="_blank">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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