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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ok…<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>So as it stands the alleles I am returning
are genomic and called via variation features. Are they always relative
to the forward strand?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
wmclaren@gmail.com [mailto:wmclaren@gmail.com] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Will McLaren<br>
<b><span style='font-weight:bold'>Sent:</span></b> 02 February 2011 16:04<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> Graham Ritchie;
dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re: [SPAM] - Re:
[SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email found in
subject - Email found in subject - Email found in subject</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Well yes, of course it depends on what you mean!<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>A transcript object in Ensembl represents the region of the genome that
generates the cDNA, not the mRNA itself - this is the only thing that we'd be
able to transfer the variation_feature object to, as I don't think there is an
Ensembl object representing the mRNA.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 2 February 2011 15:54, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName>
<<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>P.S.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Should it not be the other way around?</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>i.e. if the transcript originates from the same strand as the
variation feature then the alleles will be different? As the transcript
will be the reverse complement of the strand it originated on?</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Or have I tied my head in a knot?</span></font><o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;font-weight:
bold'>From:</span></font></b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'> <a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a>
[mailto:<a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a>]
<b><span style='font-weight:bold'>On Behalf Of </span></b>Will McLaren<br>
<b><span style='font-weight:bold'>Sent:</span></b> 02 February 2011 15:41<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> Graham Ritchie; <a
href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re: [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - Email found in subject - Email
found in subject</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>There is no direct
method to do this (if I'm following you exactly).<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>If the transcript
is on the same strand as the variation_feature (use $vf->seq_region_strand
and $transcript->seq_region_strand), then the transcript alleles will be the
same; if they are different, then you will need to reverse complement the
alleles:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>use
Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>my
$new_allele_string;<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>foreach my
$allele(split /\//, $vf->allele_string) {<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> reverse_comp($allele);<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> $new_allele_string
.= $allele.'/';<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>}<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>$new_allele_string
=~ s/\/$//;<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>We can add this
functionality as $vf->transfer() if people would find it useful.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>On 2 February 2011
15:27, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName> <<a
href="mailto:gavin.oliver@almacgroup.com" target="_blank">gavin.oliver@almacgroup.com</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>How would I go about pulling the transcriptomic one?</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;font-weight:
bold'>From:</span></font></b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'> <a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a>
[mailto:<a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a>]
<b><span style='font-weight:bold'>On Behalf Of </span></b>Will McLaren<br>
<b><span style='font-weight:bold'>Sent:</span></b> 02 February 2011 15:27<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> Graham Ritchie; <a
href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - Email found in subject</span></font><o:p></o:p></p>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>In this case, as
Graham says, the alleles will be the genomic alleles, since you are calling
from a variation_feature object.<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>On 2 February 2011
15:21, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName> <<a
href="mailto:gavin.oliver@almacgroup.com" target="_blank">gavin.oliver@almacgroup.com</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>I’m using
transcriptvariation->variation_feature->allele_string</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
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