<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">HI Maria<div><br></div><div>Yes this is expected behaviour, we don't yet support MRC5 or TIG3 cell types. You are on the right tracks for finding out what we do store. I have edited you code below to print out all the stored cell type names:</div><div><br></div><div><br></div><div><blockquote type="cite"><div><span class="Apple-tab-span" style="white-space: pre; "> </span>my @ctypes = @{$ct_adaptor->fetch_all()};</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>map { print STDOUT "**". $_->name."\n" } @ctypes;</div></blockquote></div><div><br></div><div>The 'unblessed reference' error was because you were trying to call a method on an array ref of CellType objects.</div><div><br></div><div>Hope this helps.</div><div><br></div><div><div style="font-size: 12px; ">Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Senior Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Ensembl Regulation</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><a href="http://www.ensembl.info/">http://www.ensembl.info/</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><a href="http://twitter.com/#!/ensembl">http://twitter.com/#!/ensembl</a></div><div style="font-size: 12px; "><br class="khtml-block-placeholder"></div><div style="font-size: 12px; "><br class="khtml-block-placeholder"></div><span class="Apple-style-span" style="font-size: 12px; "><br class="Apple-interchange-newline"></span></div><div><br></div><div><br><div><div>On 20 Jul 2012, at 14:18, Maria Xenophontos wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Dear developer, <div><br></div><div>I am using API version 67 and my aim is to retrieve feature sets for 3 specific cell types (IMR90, MRC5, TIG3). I try to do so by fetching the cell type by name and then fetching the feature set by CellType. The script works fine for the IMR90 cell type, however when I try to get the cell type object for MRC5 or TIG3 I get an error for uninitialized value. I have also tried to create a cell type object as follows:</div>
</blockquote><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $ctype_2= $ct_adaptor->fetch_all();</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print STDOUT "**". $ctype_2->display_label()."\n";</div>
<div><br></div><div> in order to check whether I should be passing 'MRC-5' instead of 'MRC5', but again i get an error message for calling display_label on an unblessed reference.</div><div><br></div><div>
I use the following script: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><br></div><div><div>
<span style="white-space:pre-wrap"> </span>my $ct_adaptor= $registry->get_adaptor('Human', 'funcgen', 'celltype');</div><div><span style="white-space:pre-wrap"> </span>my $ctype_1= $ct_adaptor->fetch_by_name("IMR90");</div>
<div><span style="white-space:pre-wrap"> </span></div><div><span style="white-space:pre-wrap"> </span>my @fsets;</div><div><span style="white-space:pre-wrap"> </span>my $fset_adaptor = $registry->get_adaptor( 'Human', 'funcgen', 'featureset' );</div>
<div><span style="white-space:pre-wrap"> </span>my $fsets_1= $fset_adaptor->fetch_all_by_CellType($ctype_1);</div><div><span style="white-space:pre-wrap"> </span>push @fsets, @{$fsets_1};</div><div><span style="white-space:pre-wrap"> </span></div>
</div></blockquote><div> #Works fine till here</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div> my $ctype_2= $ct_adaptor->fetch_by_name("MRC5");</div><div> my $fsets_2= $fset_adaptor->fetch_all_by_CellType($ctype_2);</div><div> push @fsets, @{$fsets_2};</div><span class="HOEnZb"><font color="#888888"><br>
</font></span></blockquote><div> I would really appreciate any comments and help on this. Thank you very much.</div><div><br></div><div>P.S.: Please ignore my previous e-mail as it was accidentally sent to you incomplete. </div>
<div><br></div><div> Kind Regards,</div><div> Maria Xenophontos </div><br><div class="gmail_quote">On Fri, Jul 20, 2012 at 2:12 PM, Maria Xenophontos <span dir="ltr"><<a href="mailto:m.xenophontos.cy@gmail.com" target="_blank">m.xenophontos.cy@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear developer, <div><br></div><div>I am using API version 67 and my aim is to retrieve feature sets for 3 specific cell types (IMR90, MRC5, TIG3). I try to do so by fetching the cell type by name and then fetching the feature set by CellType. The script works fine for the IMR90 cell type, however when I try to get the cell type object for MRC5 or TIG3 I get an error for uninitialized value</div>
<div><br></div><div><div><span style="white-space:pre-wrap"> </span>my $ct_adaptor= $registry->get_adaptor('Human', 'funcgen', 'celltype');</div><div><span style="white-space:pre-wrap"> </span>my $ctype_1= $ct_adaptor->fetch_by_name("IMR90");</div>
<div><span style="white-space:pre-wrap"> </span></div><div><span style="white-space:pre-wrap"> </span>my @fsets;</div><div><span style="white-space:pre-wrap"> </span>my $fset_adaptor = $registry->get_adaptor( 'Human', 'funcgen', 'featureset' );</div>
<div><span style="white-space:pre-wrap"> </span>my $fsets_1= $fset_adaptor->fetch_all_by_CellType($ctype_1);</div><div><span style="white-space:pre-wrap"> </span>push @fsets, @{$fsets_1};</div>
<div><span style="white-space:pre-wrap"> </span></div><div> my $ctype_2= $ct_adaptor->fetch_by_name("MRC5");</div><div> #print STDOUT "**". $ctype_2->display_label()."\n"; </div>
<div> my $fsets_2= $fset_adaptor->fetch_all_by_CellType($ctype_2);</div><div> push @fsets, @{$fsets_2};</div><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br><font color="#888888"><strong><font face="'courier new', monospace">Maria Xenophontos, BA<br>
MSc Student </font></strong><font face="'courier new', monospace"><br>School of Biological Sciences<br>University of Edinburgh <br>
</font></font><br>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#888888"><strong><font face="'courier new', monospace">Maria Xenophontos, BA<br>
MSc Student </font></strong><font face="'courier new', monospace"><br>School of Biological Sciences<br>University of Edinburgh <br>
</font></font><br>
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