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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi there.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have been trying to add a bit more functionality to the VEP script and have created a script that adds annotation to the protein annotation...<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have changed the VEP script at lines 754-757 :<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'> # protein ID<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'> if(defined $config->{protein} && $t->translation) {<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'> $line->{Extra}->{ENSP} = $t->translation->stable_id;<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'> }<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>To:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> # protein ID<o:p></o:p></p><p class=MsoNormal> if(defined $config->{protein} && $tv->transcript->translation) {<o:p></o:p></p><p class=MsoNormal> my $protein_feature_analysis = get_protein_domains($tv);<o:p></o:p></p><p class=MsoNormal> if ($protein_feature_analysis){<o:p></o:p></p><p class=MsoNormal> chomp $protein_feature_analysis;<o:p></o:p></p><p class=MsoNormal> $line->{Extra}->{ENSP} = $protein_feature_analysis;<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>And included a sub to get a bit more detail about protein domains it overlaps:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>sub get_protein_domains{<o:p></o:p></p><p class=MsoNormal> my $tv = shift;<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> ################################### protein ID ######################################################<o:p></o:p></p><p class=MsoNormal> my $translation_id = $tv->transcript->translation->stable_id;<o:p></o:p></p><p class=MsoNormal> my %protein_features =();<o:p></o:p></p><p class=MsoNormal> my $pfeatures = $tv->transcript->translation->get_all_ProteinFeatures();<o:p></o:p></p><p class=MsoNormal> foreach my $pfeature (@{$pfeatures}){<o:p></o:p></p><p class=MsoNormal> my $logic_name = $pfeature->analysis()->logic_name();<o:p></o:p></p><p class=MsoNormal> if ($pfeature->start >= $tv->transcript->translation->start && $pfeature->end <= $tv->transcript->translation->end){<o:p></o:p></p><p class=MsoNormal> $protein_features{$logic_name}{ENSP} = $translation_id || "-" ;<o:p></o:p></p><p class=MsoNormal> $protein_features{$logic_name}{interpro_ac} = $pfeature->interpro_ac() || "-";<o:p></o:p></p><p class=MsoNormal> $protein_features{$logic_name}{idesc} = $pfeature->idesc()||"-";<o:p></o:p></p><p class=MsoNormal> $protein_features{$logic_name}{start} = $pfeature->start;<o:p></o:p></p><p class=MsoNormal> $protein_features{$logic_name}{end} = $pfeature->end;<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> my $protein_feature_analysis = $translation_id;<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> for my $analysis ( keys %protein_features ){<o:p></o:p></p><p class=MsoNormal> $protein_feature_analysis .= ":".$analysis;<o:p></o:p></p><p class=MsoNormal> $protein_feature_analysis .= ",".$protein_features{$analysis}{interpro_ac};<o:p></o:p></p><p class=MsoNormal> $protein_feature_analysis .= ",".$protein_features{$analysis}{idesc};<o:p></o:p></p><p class=MsoNormal> $protein_feature_analysis .= ",".$protein_features{$analysis}{start};<o:p></o:p></p><p class=MsoNormal> $protein_feature_analysis .= ",".$protein_features{$analysis}{end}; <o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> #######################################################################################################<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> return $protein_feature_analysis;<o:p></o:p></p><p class=MsoNormal>}<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Unfortunately it seems that this annotation is only working for the mitochondrial chromosome.<o:p></o:p></p><p class=MsoNormal>Could you point me to where I might be doing something wrong?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Best regards<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='text-indent:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>