Hello,<br><br>I have something like this:<br><br><i>my $all_genomic_align_blocks = $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(<br>        $mlss, $region, undef, undef, "restrict");<br>
</i><br>  <b>  foreach my $genomic_align_block ( @{ $all_genomic_align_blocks } ) <br>{<br>   your code here??<br>}<br></b><br><br>Thanks!!!<br><br><br><div class="gmail_quote">2013/2/15 Hardip Patel <span dir="ltr"><<a href="mailto:hardip.patel@anu.edu.au" target="_blank">hardip.patel@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi<div><br></div><div>You can use something like following to remove the unwanted species.</div>
<div><br></div><div><div style="margin:0px;font-size:15px"><span style="color:#bb2ca2">foreach</span> <span style="color:#bb2ca2">my</span> $current_alignment_slice (@{$align_slice->get_all_Slices}) {</div><div style="margin:0px;font-size:15px;color:rgb(0,132,0)">
        <span style="color:rgb(187,44,162)">my</span> $name = $current_alignment_slice->genome_db->name;</div><div style="margin:0px;font-size:15px">        if ($name eq "gallus_gallus" || $name eq "meleagris_gallopavo"){</div>
<div style="margin:0px;font-size:15px">         <span style="color:#bb2ca2">my</span> $seq = $current_alignment_slice->seq;</div><div style="margin:0px;font-size:15px">          <span style="color:#bb2ca2">if</span> ($seq =~ /[ACGT]/){</div>
<div style="margin:0px;font-size:15px">            <span style="color:#bb2ca2">print</span> $gene->stable_id.<span style="color:#d12f1b">"\t"</span>.$current_alignment_slice->genome_db->taxon_id.<span style="color:#d12f1b">"\t"</span>.$current_alignment_slice->seq.<span style="color:#d12f1b">"\n"</span>;</div>
<div style="margin:0px;font-size:15px">          }</div><div style="margin:0px;font-size:15px">        }</div><div style="margin:0px;font-size:15px">}</div><div style="margin:0px;font-size:15px"><br></div><div style="margin:0px;font-size:15px">
<br></div><div style="margin:0px;font-size:15px">Cheers</div><div style="margin:0px;font-size:15px"><br></div><div style="margin:0px;font-size:15px"><br></div><div><div><div class="h5"><div>On 15/02/2013, at 9:57 AM, MARIA T. MARTÍN CAMPOS <<a href="mailto:alnitak817@gmail.com" target="_blank">alnitak817@gmail.com</a>> wrote:</div>
<br></div></div><blockquote type="cite"><div><div class="h5"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">MARIA T. MARTÍN CAMPOS</b> <span dir="ltr"><<a href="mailto:alnitak817@gmail.com" target="_blank">alnitak817@gmail.com</a>></span><br>

Date: 2013/2/14<br>Subject: API compara<br>To: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br><br><br>Good night,<br><br>my name is Trinidad Martín and I am working in a project where we have to study some sequences : anolis carolinensi, gallus gallus, meleagris_gallopavo and taeniopygia_guttata. I used a method called <b>$mlss = $mlssa->fetch_by_method_link_type_species_set_name("PECAN","amniotes");</b> and i want to align their sequencies, but just for these 4 species and $mlss contains all amniota vertebrate. I would like to know if I can find a method that returns me a $mlss just with these 4 species, searching by name maybe... or can I filter from the genomic align block??<br>


<br>Thank you very much!!<br><br>Trinidad Martín<br>
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