<div dir="ltr">Thanks Thibaut<div><br></div><div>what I want to know is: "the genomic coordinates of the clones in assembly".</div><div><br></div><div>Cheers</div><div><br></div><div>Duarte</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 7 July 2015 at 09:55, 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">Hi Duarte,<div>Sorry for the late reply. This is not a problem with the API but a data problem.</div><div>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><br></div><div>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><br></div><div>Regards</div><div><span class="HOEnZb"><font color="#888888">Thibaut</font></span><div><div class="h5"><br><div><blockquote type="cite"><div>On 7 Jul 2015, at 09:20, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Anyone? Could you help me understand why the changing behavior of the same API between datasets?</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 3 July 2015 at 17:01, 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"><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Thanks Magali</span></p><div><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><br></div><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Can you explain something
to me?</span></p><div><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><br></div><p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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> works when querying GRCh38 but fails when
querying GRCh37.</u></span></p><div><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span><br></div><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt"> </span><span style="font-size:14.6666669845581px">Shouldn't</span><span style="font-size:11pt"> 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">Isn't</span><span style="font-size:11pt"> 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"><span style="font-size:11pt"><br></span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt">Best regards</span></font></p><span><font color="#888888"><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt"><br></span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt">Duarte</span></font></p><p class="MsoNormal"><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt"><br></span></font></p></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 2 July 2015 at 16:40, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@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 bgcolor="#FFFFFF" text="#000000">
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 );<span><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></span>
Regards,<br>
Magali<div><div><br>
<br>
<div>On 01/07/2015 18:15, Duarte Molha
wrote:<br>
</div>
<blockquote 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 href="mailto:duartemolha@gmail.com" target="_blank">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>
</div>
</div>
>
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<fieldset></fieldset>
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<br></blockquote></div><br></div></div></div>
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_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div></div></div><br>_______________________________________________<br>
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<br></blockquote></div><br></div>