<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div>Cheers</div><div>Kathryn</div><div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Kathryn Beal, PhD<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge CB10 1SD, UK <br>Tel. +44 (0)1223 494458<br><a href="http://www.ensembl.org/">www.ensembl.org</a><br></div></span></div></div>
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<br><div><div>On 17 Apr 2013, at 22:11, Nathalie Conte wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div><br></div><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi, <div><br><div>I would like your help to select the more appropriate method to answer my question</div><div>From a set of mouse coordinates (chromosome start end), i would like to be able to find the equivalent orthologous coordinates in human and then find genes around (+- 2kb) and related SNPs +other variation information.</div><div>This is the start of my script below, I am parsing a mouse location file: <span style="color: rgb(4, 51, 255); font-family: Monaco; font-size: 11px; ">MouseLoctest.txt </span><span style="font-size: 11px; "><font face="Verdana">which contain my mouse coordinates</font></span> I have selected first the core API and get a slice object then I found a tutorial for getting genomic blocks from this slice- I would like to get the human coordinates (ch start end )from this block and I am not sure which method to use for this? Thanks for any suggestion-</div><div>Nathalie</div><div><span style="color: rgb(194, 27, 45); font-family: Monaco; font-size: 11px; "><br></span></div><div><font color="#c21b2d" face="Monaco"><span style="font-size: 11px;">my script so far</span></font></div><div><span style="color: rgb(194, 27, 45); font-family: Monaco; font-size: 11px; ">#!/usr/bin/perl</span></div><div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">use </span>warnings<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">use </span>strict<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="text-decoration: underline ; color: #b245f3">use </span><span style="text-decoration: underline">Bio::EnsEMBL::Registry</span><span style="text-decoration: underline ; color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">use </span>Bio::EnsEMBL::Utils::Sequence <span style="color: #b245f3">qw(reverse_comp)</span><span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="color: #b245f3">my </span><span style="">$</span><span style="color: #b237f3">registry</span><span style=""> </span><span style="color: #c13500">= </span>"Bio::EnsEMBL::Registry"<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="">$</span><span style="color: #b237f3">registry</span><span style="color: #c13500">-></span><span style="">load_registry_from_db</span><span style="color: #c13500">(-</span><span style="">host </span><span style="color: #c13500">=> </span>'<a href="http://ensembldb.ensembl.org/">ensembldb.ensembl.org</a>'<span style="color: #c13500">, -</span><span style="">user </span><span style="color: #c13500">=> </span>'anonymous'<span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); ">#input file with chromosome coordinates, open and read:</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="color: #b245f3">my </span><span style="">$</span><span style="color: #b237f3">file</span><span style=""> </span><span style="color: #c13500">= </span>"MouseLoctest.txt"<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">unless </span><span style="color: #c13500">(</span><span style="color: #b237f3">open</span><span style="color: #c13500">(</span>REGIONS<span style="color: #c13500">, </span>$<span style="color: #b237f3">file</span><span style="color: #c13500">)){</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style=""> </span><span style="color: #b237f3">print </span>"Cannot open file \"$file\"\n\n"<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(193, 53, 0); ">}</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">my </span>@<span style="color: #b237f3">regions</span> <span style="color: #c13500">= </span><REGIONS><span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b237f3">close </span>REGIONS<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="color: #b237f3">open</span><span style="color: #c13500">(</span><span style="">OUT</span><span style="color: #c13500">,</span>">test_output.txt"<span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); "># Getting the Slice adaptor:</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #b245f3">my </span><span style="">$</span>slice_adaptor<span style=""> </span><span style="color: #c13500">= </span><span style="">$</span>registry<span style="color: #c13500">-></span><span style="">get_adaptor</span><span style="color: #c13500">(</span><span style="color: #0433ff">'Mouse'</span><span style="color: #c13500">, </span><span style="color: #0433ff">'Core'</span><span style="color: #c13500">, </span><span style="color: #0433ff">'Slice'</span><span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); ">#slice obejct containing chr start and end</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #b245f3">foreach my </span><span style="">$</span>region<span style="color: #c13500">(</span><span style="">@</span>regions<span style="color: #c13500">){</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> </span>chomp <span style="">$</span>region<span style="color: #c13500">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> </span><span style="color: #b245f3">my </span><span style="">@</span>coordinates<span style=""> </span><span style="color: #c13500">= </span>split<span style="color: #c13500">(</span><span style="color: #b245f3">/\t/</span><span style="color: #c13500">, </span><span style="">$</span>region<span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> </span><span style="color: #b245f3">my </span><span style="">$</span>seq_region<span style=""> </span><span style="color: #c13500">= </span><span style="">$</span>coordinates<span style="color: #c13500">[</span><span style="color: #b23100">0</span><span style="color: #c13500">];</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> </span><span style="color: #b245f3">my </span><span style="">$</span>seq_region_start<span style=""> </span><span style="color: #c13500">= </span><span style="">$</span>coordinates<span style="color: #c13500">[</span><span style="color: #b23100">4</span><span style="color: #c13500">];</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> </span><span style="color: #b245f3">my </span><span style="">$</span>seq_region_end<span style=""> </span><span style="color: #c13500">= </span><span style="">$</span>coordinates<span style="color: #c13500">[</span><span style="color: #b23100">5</span><span style="color: #c13500">];</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(193, 53, 0); "><span class="Apple-tab-span" style="white-space:pre"> </span>};</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #b245f3">my </span><span style="">$</span>query_slice<span style=""> </span><span style="color: #c13500">=</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="">$</span>slice_adaptor<span style="color: #c13500">-></span><span style="">fetch_by_region</span><span style="color: #c13500">(</span><span style="color: #0433ff">'chromosome'</span><span style="color: #c13500">,</span><span style="">$</span>seq_region<span style="color: #c13500">,</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="">$</span>seq_region_start<span style="color: #c13500">, </span><span style="">$</span>seq_region_end<span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="">throw</span><span style="color: #c13500">(</span>"No Slice can be created with coordinates</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); ">$seq_region:$seq_region_start-"<span style="color: #c13500">.</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style=""> </span>"$seq_region_end"<span style="color: #c13500">) </span><span style="color: #b245f3">if </span><span style="color: #c13500">(</span><span style="">!$</span><span style="color: #b237f3">query_slice</span><span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); ">#now go wit this splice to compara and fetch the corresponding human sequence from this slice</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); "># Getting the GenomicAlignBlock adaptor:</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #b245f3">my </span>$<span style="color: #b237f3">genomic_align_block_adaptor</span> <span style="color: #c13500">= </span>Bio::EnsEMBL::Registry<span style="color: #c13500">-></span>get_adaptor<span style="color: #c13500">(</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style=""> </span>'Multi'<span style="color: #c13500">, </span>'compara'<span style="color: #c13500">, </span>'GenomicAlignBlock'<span style="color: #c13500">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); "># Fetching all the GenomicAlignBlock corresponding to this Slice:</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #b245f3">my </span><span style="">$</span>genomic_align_blocks<span style=""> </span><span style="color: #c13500">=</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "> $<span style="color: #b237f3">genomic_align_block_adaptor</span><span style="color: #c13500">-></span>fetch_all_by_MethodLinkSpeciesSet_Slice<span style="color: #c13500">(</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> $</span>human_mouse_blastz_net_mlss<span style="color: #c13500">,</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style=""> $</span>query_slice<span style="color: #c13500">);</span></div></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #c13500"><br></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: #c13500">I am stuck here and would like the coordinates ??</span></div><div><div style="text-align: left; "> <br class="webkit-block-placeholder"></div><br>
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