<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Duarte,<div class=""><br class=""></div><div class="">we do have code that deals with a slightly different version of your use case. The <a href="https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/TranscriptHaplotypeContainer.pm#L1157-L1160" class="">code</a> we have constructs transcript haplotypes from phased variants. You could take a look and see if you could extract some of the code for your use case. But at the moment I cannot point you to any API function that could help you with your use case.</div><div class=""><br class=""></div><div class="">Kind regards,</div><div class="">Anja</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 5 Mar 2018, at 14:49, Duarte Molha <<a href="mailto:duartemolha@gmail.com" class="">duartemolha@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi guys<div class=""><br class=""></div><div class="">I was wondering if I could get some pointers from you about the best way to accomplish a task.</div><div class=""><br class=""></div><div class="">I have a genomic slice and an array of variations features that overlap that slice</div><div class=""><br class=""></div><div class="">Is there a elegant way of modifying the slice sequence to incorporate one or more of the alternative alleles of each variant without doing a bunch of substring concatenations?</div><div class=""><br class=""></div><div class="">for example for the sake of simplicity I have a 10 bp slice sequence on chr1:100-110 bp</div><div class=""><br class=""></div><div class="">AATTAGTATG</div><div class=""><br class=""></div><div class="">and I have a known variant at position 102 A/T<br class=""></div><div class=""><br class=""></div><div class="">my required outcome would be </div><div class=""><br class=""></div><div class="">
<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">A</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><b class="">[T]</b></span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">TTAGTATG => <span style="font-weight:400;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">A</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">T</span><span style="font-weight:400;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">TTAGTATG<span class=""> </span></span> </span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">Ideally I would like to use the Perl api where possible and be able to generalise this process as best as possible so that i can input a variable number of variants of different types </span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">For example, say that on the same 10 bp sequence I had 2 variations and one was a 1bp deletion:</span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class="">AATTAGTATG <br class=""></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class="">var 1 pos 102 [A/T]</div><div class="">var2 pos 106 [G/-]</div><div class=""><br class=""></div><div class="">the output would be </div><div class=""><br class=""></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""> <span style="font-weight:400;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">A[</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><b class="">T]</b></span><span style="font-weight:400;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">TTA[-]TATG</span> => <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">A</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><b class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">T</span></b></span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">TTATATG</span> <br class=""></span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">Any suggestions?</span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class="">Many thanks</span></div><div class=""><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline" class=""><br class=""></span></div><div class="">Duarte</div><div class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""></div></div></div>
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