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PFPmatrix- use different bits for newly added dbnsfp scores #1191

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Merged
merged 2 commits into from
Oct 23, 2025
Merged

PFPmatrix- use different bits for newly added dbnsfp scores #1191

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0934613
PFPmatrix- use different bits for newly added dbnsfp scores
nakib103 Oct 22, 2025
2eedc79
Revert back unit test changes
nakib103 Oct 22, 2025
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24 changes: 16 additions & 8 deletions modules/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -166,15 +166,23 @@ my $BYTES_PER_PREDICTION = 2;

# constants derived from the the user-defined constants

# the maximum number of distinct qualitative predictions used by any tool

my $MAX_NUM_PREDS = max( map { scalar keys %$_ } values %$PREDICTION_TO_VAL );

# the number of bits used to encode the qualitative prediction

my $NUM_PRED_BITS = ceil( log($MAX_NUM_PREDS) / log(2) );
# my $NUM_PRED_BITS = ceil( log($MAX_NUM_PREDS) / log(2) );
my $NUM_PRED_BITS = {
polyphen => 2,
sift => 2,
cadd => 2,
dbnsfp_revel => 2,
dbnsfp_alphamissense => 3,
dbnsfp_esm1b => 3,
dbnsfp_meta_lr => 2,
dbnsfp_mutation_assessor => 2
};

throw("Cannot represent more than ".(2**6-1)." predictions") if $NUM_PRED_BITS > 6;
# the maximum number of distinct qualitative predictions used by any tool
my $MAX_NUM_PREDS = max( values %$NUM_PRED_BITS );
throw("Cannot represent more than ".(2**6-1)." predictions") if $MAX_NUM_PREDS > 6;

# a hash mapping back from a numerical value to a qualitative prediction

Expand Down Expand Up @@ -549,7 +557,7 @@ sub prediction_to_short {
throw("No value defined for prediction: '$pred'?")
unless defined $pred_val;

$val |= ($pred_val << (16 - $NUM_PRED_BITS));
$val |= ($pred_val << (16 - $NUM_PRED_BITS->{$self->{analysis}}));

printf("p2s: $pred ($prob) => 0x%04x\n", $val) if $DEBUG;

Expand Down Expand Up @@ -584,7 +592,7 @@ sub prediction_from_short {

# shift the prediction bits down and look up the prediction string

my $pred = $VAL_TO_PREDICTION->{$self->{analysis}}->{$val >> (16 - $NUM_PRED_BITS)};
my $pred = $VAL_TO_PREDICTION->{$self->{analysis}}->{$val >> (16 - $NUM_PRED_BITS->{$self->{analysis}})};

# mask off the top 6 bits reserved for the prediction and convert back to a 3 d.p. float

Expand Down
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