<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Duarte,<div class="">Sorry for the late reply. This is not a problem with the API but a data problem.</div><div class="">When you do the call $mf_adaptor->fetch_all_by_attribute_type_value( 'Name', $query ) you're asking for all the clones (misc features) which have the attribute 'Name'. So if we haven't store any data with this attribute, the API will return nothing but it will have done it's job. We used a different attribute in this case which was a error. It will be fixed for release 82. Sorry for the problem it's causing you.</div><div class=""><br class=""></div><div class="">Before replying to your previous question about my code snippet, I may have misunderstood what you wanted to do. By printing the clone coordinates, do you want to know the coordinates of the clones in the assembly or do you want to know where the clones overlap the assembly (this is what the tilepath is)?</div><div class=""><br class=""></div><div class="">Regards</div><div class="">Thibaut<br class=""><div><blockquote type="cite" class=""><div class="">On 7 Jul 2015, at 09:20, 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="">Anyone? Could you help me understand why the changing behavior of the same API between datasets?</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 3 July 2015 at 17:01, 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=""><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class="">Thanks Magali</span></p><div class=""><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class="">Can you explain something
to me?</span></p><div class=""><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class="">You are now keeping the api compatible with both GRCH37 and GRCH38. This is great because I can use my
scripts with the latest API and not worry about having to use an older API to
query the older assembly. However I do not understand why, in this case
changing ‘clone_name’ to ‘Name’<u class=""> works when querying GRCh38 but fails when
querying GRCh37.</u></span></p><div class=""><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class=""> </span><span style="font-size:14.6666669845581px" class="">Shouldn't</span><span style="font-size:11pt" class=""> the API calls be the same for both
datasets. This means I have to change my code depending on what database I am querying. </span><span style="font-size:14.6666669845581px" class="">Isn't</span><span style="font-size:11pt" class=""> this what the move to update the api for both datasets is trying to avoid?</span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class=""><br class=""></span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class="">Best regards</span></font></p><span class="HOEnZb"><font color="#888888" class=""><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class=""><br class=""></span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class="">Duarte</span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif" class=""><span style="font-size:11pt" class=""><br class=""></span></font></p></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 2 July 2015 at 16:40, mag <span dir="ltr" class=""><<a href="mailto:mr6@ebi.ac.uk" target="_blank" class="">mr6@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">
<div bgcolor="#FFFFFF" text="#000000" class="">
Hi Duarte,<br class="">
<br class="">
Replacing 'clone_name' with 'Name' as Thibaut suggested works for me
for GRCh38.<br class="">
<br class="">
my $clones = $mf_adaptor->fetch_all_by_attribute_type_value(
'Name', $query );<span class=""><br class="">
<br class="">
while ( my $clone = shift @{$clones} ) {<br class="">
my $slice = $clone->slice();<br class="">
print join "\t", ("chr".$slice->seq_region_name(),
$clone->start(), $clone->end() , $query."\n");<br class="">
}<br class="">
<br class="">
<br class=""></span>
Regards,<br class="">
Magali<div class=""><div class=""><br class="">
<br class="">
<div class="">On 01/07/2015 18:15, Duarte Molha
wrote:<br class="">
</div>
<blockquote type="cite" class=""><p dir="ltr" class="">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" target="_blank" class="">duartemolha@gmail.com</a>>
wrote:<br type="attribution" class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Thibaut... Could you expand on how I can change my
script to make it work with the new assembly?</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Can you tell me how I can modify my script to work with
the new assembly?</div>
<div class=""><br class="">
</div>
<div class="">I don't seem to understand the projection method you
are using.<br class="">
</div>
<div class="">Here is the relevant part of my script </div>
<div class=""><br class="">
</div>
<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){</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>chomp
$query;</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>my $clones
= $mf_adaptor->fetch_all_by_attribute_type_value(
'clone_name', $query );</div>
<div class=""><br class="">
</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>while ( my
$clone = shift @{$clones} ) {</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>my $slice =
$clone->slice();</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>print join
"\t", ("chr".$slice->seq_region_name(),
$clone->start(), $clone->end() , $query."\n"); </div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>}</div>
<div class="">}</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=""><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 15:46, 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="">no. That does not get anything.
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</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="">
<div class="gmail_quote">On 30 June 2015 at 14:50,
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">
<div style="word-wrap:break-word" class="">If you use
name instead of clone_name, does it fetches
the missing one?
<div class=""><br class="">
</div>
<div class="">Cheers</div>
<span class=""><font color="#888888" class="">
<div class="">Thibaut</div>
</font></span>
<div class="">
<div class="">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Jun 2015, at 14:27,
Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank" class="">duartemolha@gmail.com</a>>
wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">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 class="">However... can you please
answer my question regarding
the missing clones like <span style="font-size:11.9999990463257px" class=""> </span><span style="font-size:11.9999990463257px" class="">RP11-155D3
... why can I not fetch
this when it is clearly on
the database?</span></div>
<div class=""><span style="font-size:11.9999990463257px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:11.9999990463257px" class="">Thanks</span></div>
<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=""><b class=""><br class="">
</b></div>
</div>
<div class="gmail_extra"><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="">
<div class="gmail_quote">On 30
June 2015 at 14:12, 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">
<div style="word-wrap:break-word" 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>
<span class=""><font color="#888888" class="">
<div class="">Thibaut</div>
</font></span>
<div class="">
<div class="">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Jun
2015, at
13:56, Duarte
Molha <<a href="mailto:duartemolha@gmail.com" target="_blank" class="">duartemolha@gmail.com</a>>
wrote:</div>
<br class="">
<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 style="white-space:pre-wrap" class="">
</span>chomp
$query;</div>
<div class=""><span style="white-space:pre-wrap" class="">
</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 style="white-space:pre-wrap" class="">
</span>while (
my $clone =
shift
@{$clones} ) {</div>
<div class=""><span style="white-space:pre-wrap" class="">
</span>my
$slice =
$clone->slice();</div>
<div class=""><span style="white-space:pre-wrap" class="">
</span>print
join "\t",
("chr".$slice->seq_region_name(),
$clone->start(),
$clone->end()
,
$query."\n"); </div>
<div class=""><span style="white-space:pre-wrap" class="">
</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=""><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=""><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="">
<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>
>
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mailing list
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guidelines and
subscribe/unsubscribe
info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">
> Ensembl
Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank" class="">http://www.ensembl.info/</a><br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
Dev mailing
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Posting
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Ensembl Blog:
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</blockquote>
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<br class="">
<fieldset class=""></fieldset>
<br class="">
<pre class="">_______________________________________________
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<br class=""></blockquote></div><br class=""></div></div></div>
</blockquote></div><br class=""></div>
_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div></body></html>