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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'>Thanks Will – that has done the trick!<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'>Best, <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'>Gavin<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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<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> 26 January 2011 13:11<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> dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re:
[ensembl-dev] Converting genomic coordinates to transcript coordinates - 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'>Hi Gavin,<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>You will need a transcript mapper object:<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>my $tm = $transcript->get_TranscriptMapper;<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>my @coords = $tm->genomic2cdna($start, $end, $strand);<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>This returns a list of Bio::EnsEMBL::Mapper::Coordinate and
<meta charset=utf-8>
Bio::EnsEMBL::Mapper::Gap objects.<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Cheers<o:p></o:p></span></font></p>
</div>
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<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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<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 26 January 2011 12:46, <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=purple>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Hi, </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>I’m guessing
the answer will be transfer or transform but can someone advise on the fastest
way to convert feature start/end coordinates from genomic to
transcript-based? I don’t want to mistakenly do it in an unnecessarily
time/resource-consuming manner.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Best, </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:150%'><font size=2 face=Arial><span style='font-size:10.0pt;
line-height:150%;font-family:Arial'>Gavin</span></font><o:p></o:p></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'> <o:p></o:p></span></font></p>
</div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'>Almac Group (UK) Limited, registered no. NI061368.
Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited,
registered no. NI046249. Almac Pharma Services Limited, registered no.
NI045055. Almac Clinical Services Limited, registered no. NI041905.
Almac Clinical Technologies Limited, registered no. NI061202. Almac
Diagnostics Limited, registered no. NI043067. All preceding companies are
registered in <st1:country-region w:st="on">Northern Ireland</st1:country-region>
with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place
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5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>.
</span></font><o:p></o:p></p>
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Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region>
no. SC154034. </span></font><o:p></o:p></p>
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size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'>Almac Clinical Services LLC, Almac Clinical Technologies
LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC
are <st1:State w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:State>
limited liability companies and Almac Group Incorporated is a Delaware
Corporation. More information on the Almac Group can be found on the
Almac website: <a href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a></span></font><o:p></o:p></p>
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face="Times New Roman"><span style='font-size:12.0pt'><br>
_______________________________________________<br>
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<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: <A href="http://www.almacgroup.com">www.almacgroup.com</A><o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
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