<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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>.$current_alignment_slice->seq.<span style="color: #d12f1b">"\n"</span>;</div><div style="margin: 0px; font-size: 15px; "> }</div><div style="margin: 0px; font-size: 15px; "> }</div><div style="margin: 0px; font-size: 15px; ">}</div><div style="margin: 0px; font-size: 15px; "><br></div><div style="margin: 0px; font-size: 15px; "><br></div><div style="margin: 0px; font-size: 15px; ">Cheers</div><div style="margin: 0px; font-size: 15px; "><br></div><div style="margin: 0px; font-size: 15px; "><br></div><div><div>On 15/02/2013, at 9:57 AM, MARIA T. MARTÍN CAMPOS <<a href="mailto:alnitak817@gmail.com">alnitak817@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">MARIA T. MARTÍN CAMPOS</b> <span dir="ltr"><<a href="mailto:alnitak817@gmail.com">alnitak817@gmail.com</a>></span><br>
Date: 2013/2/14<br>Subject: API compara<br>To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br><br><br>Good night,<br><br>my name is Trinidad Martín and I am working in a project where we have to study some sequences : anolis carolinensi, gallus gallus, meleagris_gallopavo and taeniopygia_guttata. I used a method called <b>$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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