<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 12pt;
font-family:Calibri
}
--></style></head>
<body class='hmmessage'><div dir='ltr'>Hi All,<BR>
<BR>
I am writing some code right now that uses Members, GeneMembers and SeqMembers. Is it true that the Member is being deprecated in the upcoming Ensembl 76 release? <BR>
<BR>
If so, <BR>
<BR>
1) Almost all of the relevant examples use what may soon be deprecated code. FOr instance <A href="http://useast.ensembl.org/info/docs/api/compara/compara_tutorial.html">http://useast.ensembl.org/info/docs/api/compara/compara_tutorial.html</A> has the stanza of code below just after a stanza example that has GeneMember objects. <BR>
<SPAN class="comp_tut kwc">my</SPAN> <SPAN class="comp_tut kwb">$homology</SPAN> <SPAN class="comp_tut opt">=</SPAN> <SPAN class="comp_tut kwb">$homologies</SPAN><SPAN class="comp_tut opt">->[</SPAN><SPAN class="comp_tut num">0</SPAN><SPAN class="comp_tut opt">];</SPAN> <SPAN class="comp_tut slc"># take one of the homologies and look into it</SPAN><BR><SPAN class="comp_tut kwa">foreach</SPAN> <SPAN class="comp_tut kwc">my</SPAN> <SPAN class="comp_tut kwb">$member</SPAN> <SPAN class="comp_tut opt">(</SPAN>@<SPAN class="comp_tut opt">{</SPAN><SPAN class="comp_tut kwb">$homology</SPAN><SPAN class="comp_tut opt">-></SPAN><SPAN class="comp_tut kwd">get_all_Members</SPAN><SPAN class="comp_tut opt">}) {</SPAN><BR> <SPAN class="comp_tut slc"># each AlignedMember contains both the information on the SeqMember and in</SPAN><BR> <SPAN class="comp_tut slc"># relation to the homology</SPAN><BR> <SPAN class="comp_tut kwc">print</SPAN> <SPAN class="comp_tut opt">(</SPAN><SPAN class="comp_tut kwc">join</SPAN> <SPAN class="comp_tut str">" "</SPAN><SPAN class="comp_tut opt">,</SPAN> <SPAN class="comp_tut kwc">map</SPAN> <SPAN class="comp_tut opt">{</SPAN> <SPAN class="comp_tut kwb">$member</SPAN><SPAN class="comp_tut opt">-></SPAN><SPAN class="comp_tut kwb">$_</SPAN> <SPAN class="comp_tut opt">}</SPAN> <SPAN class="comp_tut kwc">qw</SPAN><SPAN class="comp_tut opt">(</SPAN>stable_id taxon_id<SPAN class="comp_tut opt">)).</SPAN><SPAN class="comp_tut str">"</SPAN><SPAN class="comp_tut esc">\n</SPAN><SPAN class="comp_tut str">"</SPAN><SPAN class="comp_tut opt">;</SPAN><BR> <SPAN class="comp_tut kwc">print</SPAN> <SPAN class="comp_tut opt">(</SPAN><SPAN class="comp_tut kwc">join</SPAN> <SPAN class="comp_tut str">" "</SPAN><SPAN class="comp_tut opt">,</SPAN> <SPAN class="comp_tut kwc">map</SPAN> <SPAN class="comp_tut opt">{</SPAN> <SPAN class="comp_tut kwb">$member</SPAN><SPAN class="comp_tut opt">-></SPAN><SPAN class="comp_tut kwb">$_</SPAN> <SPAN class="comp_tut opt">}</SPAN> <SPAN class="comp_tut kwc">qw</SPAN><SPAN class="comp_tut opt">(</SPAN>perc_id perc_pos perc_cov<SPAN class="comp_tut opt">)).</SPAN><SPAN class="comp_tut str">"</SPAN><SPAN class="comp_tut esc">\n</SPAN><SPAN class="comp_tut str">"</SPAN><SPAN class="comp_tut opt">;</SPAN><BR><SPAN class="comp_tut opt">}</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<SPAN class="comp_tut opt">2) Will get_all_Members still be available after r75?</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<SPAN class="comp_tut opt">3) Is there any plan on adjusting the tutorials etc. for GeneMembers and SeqMembers?</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<SPAN class="comp_tut opt">4) How different will the Compara API be in r76? Again, I am currently writing code to try to take advantage of what I understand to be more Compara data in r76 but I am concerned the API will be different and I will have to re-write.</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<SPAN class="comp_tut opt">So many questions, I know, but is there some guidance you could give on the topic of Compara API changes and deprecations coming in ensembl 76?</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<SPAN class="comp_tut opt">Many, many thanks,</SPAN><BR>
<SPAN class="comp_tut opt">Ed</SPAN><BR>
<SPAN class="comp_tut opt"></SPAN> <BR>
<BR><BR><BR> </div></body>
</html>