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Hi Duarte,<br>
<br>
Replacing 'clone_name' with 'Name' as Thibaut suggested works for me
for GRCh38.<br>
<br>
my $clones = $mf_adaptor->fetch_all_by_attribute_type_value(
'Name', $query );<br>
<br>
while ( my $clone = shift @{$clones} ) {<br>
my $slice = $clone->slice();<br>
print join "\t", ("chr".$slice->seq_region_name(),
$clone->start(), $clone->end() , $query."\n");<br>
}<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 01/07/2015 18:15, Duarte Molha
wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoE+xY+OsGoR+-1DJdDK+6jCDXJEnh2yQ2-S+o297FVYWEA@mail.gmail.com"
type="cite">
<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
moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true" 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 moz-do-not-send="true"
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
moz-do-not-send="true" 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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://about.me/duarte" rel="noreferrer" target="_blank">http://about.me/duarte</a><br>
>
=========================<br>
><br>
</div>
</div>
>
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