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Add pick_count option - number of results to return by pick #1733

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Add pick_count option - number of results to return by pick #1733

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53e3568
Add pick_count option - number of results to return by pick
nakib103 Aug 7, 2024
038ab99
Add default value
nakib103 Aug 7, 2024
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2 changes: 2 additions & 0 deletions modules/Bio/EnsEMBL/VEP/Config.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,7 @@ our @VEP_PARAMS = (
'flag_pick_allele_gene', # flag one con per gene, allele
'flag_gencode_primary', # flag gencode primary transcripts
'pick_order=s', # define the order of categories used by the --*pick* flags
'pick_count=i', # define the number of transcripts to return used by the --*pick* flags
'buffer_size=i', # number of variations to read in before analysis
'failed=i', # include failed variations when finding existing
'gp', # read coords from GP part of INFO column in VCF (probably only relevant to 1KG)
Expand Down Expand Up @@ -303,6 +304,7 @@ our %DEFAULTS = (
core_type => 'core',
polyphen_analysis => 'humvar',
pick_order => [qw(mane_select mane_plus_clinical canonical appris tsl biotype ccds rank length ensembl refseq )],
pick_count => 1,
terminal_width => 48,
vcf_info_field => 'CSQ',
ucsc_data_root => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
Expand Down
16 changes: 6 additions & 10 deletions modules/Bio/EnsEMBL/VEP/OutputFactory.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -150,6 +150,7 @@ sub new {
output_format
no_escape
pick_order
pick_count
allele_number
show_ref_allele
use_transcript_ref
Expand Down Expand Up @@ -769,7 +770,7 @@ sub pick_worst_VariationFeatureOverlapAllele {
push @vfoa_info, $info;
}
if(scalar @vfoa_info) {
my @order = @{$self->{pick_order}};
my @order = reverse @{$self->{pick_order}};
my $picked;

# go through each category in order
Expand All @@ -793,17 +794,12 @@ sub pick_worst_VariationFeatureOverlapAllele {
# now add to @tmp those vfoas that have the same value self $cat as $picked
push @tmp, shift @vfoa_info while @vfoa_info && $vfoa_info[0]->{$cat} eq $picked->{$cat};

# if there was only one, return
return $picked->{vfoa} if scalar @tmp == 1;

# otherwise shrink the array to just those that had the lowest
# this gives fewer to sort on the next round
@vfoa_info = @tmp;

# if there are sufficient transcripts, return
return map {$_->{vfoa}} @tmp if scalar @tmp == $self->pick_count;
}

# probably shouldn't get here, but if we do, return the first
return $vfoa_info[0]->{vfoa};
# return the number of picK_count transcript
return map {$_->{vfoa}} @vfoa_info[0..($self->pick_count-1)];
}

return undef;
Expand Down