<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_ym19_1_1499695086217_14602" dir="ltr"><span id="yui_3_16_0_ym19_1_1499695086217_15565">Thanks everybody for your replies. I think Lenna's code would work best, and I agree with Peter that it would be good to have this functionality included in Biopython.</span></div><div dir="ltr" id="yui_3_16_0_ym19_1_1499695086217_15861"><span id="yui_3_16_0_ym19_1_1499695086217_15565">I could get Lenna's code to work with transcript positions (i.e. cmap.c2g(position)), but as far as I can tell it currently does not handle ranges, i.e. cmap.c2g([start, end]), which gets tricky if the range spans an exon-exon boundary. <br></span></div><div dir="ltr" id="yui_3_16_0_ym19_1_1499695086217_15860"><span id="yui_3_16_0_ym19_1_1499695086217_15565">Her code looks well-written, with plenty of test cases, however I feel that the module would need a dedicated maintainer for it to be viable long-term in Biopython.<br></span></div><div dir="ltr" id="yui_3_16_0_ym19_1_1499695086217_15859"><span id="yui_3_16_0_ym19_1_1499695086217_15565"><br></span></div><div dir="ltr" id="yui_3_16_0_ym19_1_1499695086217_15828"><span id="yui_3_16_0_ym19_1_1499695086217_15565">Thanks again,</span></div><div dir="ltr" id="yui_3_16_0_ym19_1_1499695086217_15858"><span id="yui_3_16_0_ym19_1_1499695086217_15565">-Michiel</span></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> On Thursday, July 6, 2017 7:22 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div dir="ltr">Hi all,<br clear="none"><br clear="none">A while back Lenna submitted a pull request which should be of interest:<br clear="none"><br clear="none"><a shape="rect" href="https://github.com/biopython/biopython/pull/309" target="_blank">https://github.com/biopython/biopython/pull/309</a><br clear="none"><br clear="none">Documentation:<br clear="none"><br clear="none"><a shape="rect" href="http://biopython.org/wiki/Coordinate_mapping" target="_blank">http://biopython.org/wiki/Coordinate_mapping</a><br clear="none"><br clear="none">Example:<br clear="none"><br clear="none"><a shape="rect" href="https://gist.github.com/lennax/10600113" target="_blank">https://gist.github.com/lennax/10600113</a><br clear="none"><br clear="none">Having a fresh set of eyes on this would be great, as there does<br clear="none">seem to be enough interest to finish this and get it added to<br clear="none">Biopython.<br clear="none"><br clear="none">Thanks,<br clear="none"><br clear="none">Peter<br clear="none"><br clear="none">On Thu, Jul 6, 2017 at 10:42 AM, Gerard Schaafsma<br clear="none"><<a shape="rect" ymailto="mailto:gerard.schaafsma@med.lu.se" href="mailto:gerard.schaafsma@med.lu.se">gerard.schaafsma@med.lu.se</a>> wrote:<br clear="none">> Hi,<br clear="none">><br clear="none">> Did you have a look at <a shape="rect" href="https://mutalyzer.nl/" target="_blank">https://mutalyzer.nl </a>? There is a position converter<br clear="none">> in there.<br clear="none">><br clear="none">> Best,<br clear="none">><br clear="none">> Gerard<br clear="none">><br clear="none">><br clear="none">> On 05/07/17 12:04, Michiel de Hoon wrote:<br clear="none">><br clear="none">> Dear all,<br clear="none">><br clear="none">> Does anybody have some code to convert transcript coordinates to genome<br clear="none">> coordinates?<br clear="none">> I have the position of a nucleotide along a transcript, and the genome<br clear="none">> coordinates of the start and end of each exon in the transcript, and I would<br clear="none">> like to find the position of the nucleotide in genome coordinates.<br clear="none">> Ideally, I am looking for some code that can find the genome coordinates of<br clear="none">> a sequence of nucleotides.<br clear="none">> For example, if these are the exons:<br clear="none">> exon1 10000 10030<br clear="none">> exon2 10050 10080<br clear="none">> and a nucleotide sequence starting at position 20 and ending at position 50<br clear="none">> in transcript coordinates,<br clear="none">> then I am looking for the genome coordinates (10020,10030), (10050,10070).<br clear="none">><br clear="none">> Thanks,<br clear="none">> -Michiel<br clear="none">><br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br clear="none">><br clear="none">><br clear="none">> --<br clear="none">> Gerard C.P. Schaafsma<br clear="none">> Protein Structure and Bioinformatics Group<br clear="none">> Dept. of Experimental Medical Science<br clear="none">> Lund University<br clear="none">> BMC B13, Hs 66<br clear="none">> 221 84 Lund<br clear="none">> Sweden<div class="yqt0389888502" id="yqtfd03839"><br clear="none">><br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none">> <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br clear="none">_______________________________________________<br clear="none">Biopython mailing list - <a shape="rect" ymailto="mailto:Biopython@mailman.open-bio.org" href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br clear="none"><a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br clear="none"></div></div><br><br></div> </div> </div> </div></div></body></html>