[ensembl-dev] undefined MAF values

[Jens Christian Nielsen]

Hi Ensemblers,

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.

/Jens

my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
['missense_variant'])};
foreach my $vf (@vfs) {
my $transcript_variations = $vf->get_all_TranscriptVariations;
 if (defined $transcript_variations){
foreach my $tv (@{$transcript_variations}){
if (defined $tv->pep_allele_string) { # the AA change
print $tv->pep_allele_string . "\t";
} else { print "undef \t"; }
if (defined $tv->translation_start ) {
print $tv->translation_start,'-',$tv->translation_end,"\t"; # AA position
in protein
} else { print "undef \t"; }
if (defined $vf->minor_allele_frequency ) {
print $vf->minor_allele_frequency . "\n"; # the Minor Allele Frequency
} else { print "undef \n"; }
}
}
}
>>> perl missens_freq.pl
aa change position Minor allele freq
-----------------------------------------
R/Q 64-64   undef
R/Q 64-64   undef
R/Q     64-64   undef
R/W     64-64   undef
R/W     64-64   undef
R/W     64-64   undef
P/T     46-46   undef
P/T     46-46   undef
P/T     46-46   undef
G/E     40-40   undef
G/E     40-40   undef
G/E     40-40   undef
S/F     32-32   undef
S/F     32-32   undef
S/F     32-32   undef
S/L     25-25   undef
S/L     25-25   undef
S/L     25-25   undef
K/R     17-17   0.0027
K/R     17-17   0.0027
K/R     17-17   0.0027
I/T     6-6     0.0856
I/T     6-6     0.0856
I/T     6-6     0.0856
S/F     3-3     undef
S/F     3-3     undef
S/F     3-3     undef
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