<div>Hi Ensemblers,</div><div><br></div><div>I have made a script extracting missense mutations and their frequencies of different human proteins through the perl api. Below is shown the core of the script as well as the output. My question goes to the output, which contain an awfull lot of "undefined" especially for the frequencies (MAF), but also in some cases for the two other parameters (aa change, and postion). Do I do something wrong to get all those undef, or is it just the DB that is missing some information? Also, why does the script produce multiples of the same output (many lines are the same)? I am not specifying it to return anything more than once.</div>
<div><br></div><div>/Jens</div><div><br></div><div>my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice, ['missense_variant'])};</div><div><span class="Apple-tab-span" style="white-space:pre"> </span></div><div>
foreach my $vf (@vfs) {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $transcript_variations = $vf->get_all_TranscriptVariations;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>if (defined $transcript_variations){</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>foreach my $tv (@{$transcript_variations}){</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>if (defined $tv->pep_allele_string) { # the AA change</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print $tv->pep_allele_string . "\t";</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>} else { print "undef \t"; }</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if (defined $tv->translation_start ) {</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>print $tv->translation_start,'-',$tv->translation_end,"\t"; # AA position in protein</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>} else { print "undef \t"; }</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>if (defined $vf->minor_allele_frequency ) {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print $vf->minor_allele_frequency . "\n"; # the Minor Allele Frequency</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>} else { print "undef \n"; }</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>}</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>}</div>
<div>}</div><div>>>> perl <a href="http://missens_freq.pl">missens_freq.pl</a></div><div>aa change<span class="Apple-tab-span" style="white-space:pre"> </span>position<span class="Apple-tab-span" style="white-space:pre"> </span>Minor allele freq</div>
<div>-----------------------------------------</div><div>R/Q<span class="Apple-tab-span" style="white-space:pre"> </span>64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>R/Q <span class="Apple-tab-span" style="white-space:pre"> </span>64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>R/Q <span class="Apple-tab-span" style="white-space:pre"> </span> 64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>R/W <span class="Apple-tab-span" style="white-space:pre"> </span>64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>R/W <span class="Apple-tab-span" style="white-space:pre"> </span>64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>R/W <span class="Apple-tab-span" style="white-space:pre"> </span>64-64 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>P/T <span class="Apple-tab-span" style="white-space:pre"> </span>46-46 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>P/T <span class="Apple-tab-span" style="white-space:pre"> </span>46-46 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>P/T <span class="Apple-tab-span" style="white-space:pre"> </span>46-46 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>G/E <span class="Apple-tab-span" style="white-space:pre"> </span>40-40 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>G/E <span class="Apple-tab-span" style="white-space:pre"> </span>40-40 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>G/E <span class="Apple-tab-span" style="white-space:pre"> </span>40-40 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>32-32 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>32-32 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>32-32 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>S/L <span class="Apple-tab-span" style="white-space:pre"> </span>25-25 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>S/L <span class="Apple-tab-span" style="white-space:pre"> </span>25-25 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>S/L <span class="Apple-tab-span" style="white-space:pre"> </span>25-25 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>K/R <span class="Apple-tab-span" style="white-space:pre"> </span>17-17 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0027</div><div>K/R <span class="Apple-tab-span" style="white-space:pre"> </span>17-17 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0027</div>
<div>K/R <span class="Apple-tab-span" style="white-space:pre"> </span>17-17 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0027</div><div>I/T <span class="Apple-tab-span" style="white-space:pre"> </span>6-6 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0856</div>
<div>I/T <span class="Apple-tab-span" style="white-space:pre"> </span>6-6 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0856</div><div>I/T <span class="Apple-tab-span" style="white-space:pre"> </span>6-6 <span class="Apple-tab-span" style="white-space:pre"> </span>0.0856</div>
<div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>3-3 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>3-3 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div>
<div>S/F <span class="Apple-tab-span" style="white-space:pre"> </span>3-3 <span class="Apple-tab-span" style="white-space:pre"> </span>undef </div><div><br></div>