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@adthrasher
adthrasher committed Jul 12, 2021
1 parent 1496f2b commit 6750da4
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Showing 4 changed files with 28 additions and 70 deletions.
12 changes: 12 additions & 0 deletions src/perllib/CiceroUtil.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -823,6 +823,18 @@ sub normalizeChromosomeName {
return $query;
}

sub exist_multiplename_checking {
my %genelist = %{(shift)};
my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
my @genes = split(/,|\|/, $targetgene);

foreach my $g1 (@genes) {
return 1 if(exists($genelist{$g1}));
}

return 0;
}

1;

=head1 LICENCE AND COPYRIGHT
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42 changes: 6 additions & 36 deletions src/scripts/annotate.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

use CiceroSCValidator qw($lowqual_cutoff LEFT_CLIP RIGHT_CLIP);
use CiceroUtil qw(prepare_reads_file parse_range rev_comp
is_PCR_dup read_fa_file get_discordant_reads get_sclip_reads normalizeChromosomeName);
is_PCR_dup read_fa_file get_discordant_reads get_sclip_reads normalizeChromosomeName exist_multiplename_checking);

require CiceroExtTools;

Expand All @@ -27,6 +27,8 @@
use Gene;
use GeneModel;

use constant BADFUSION_DISTANCE_CUTOFF => 200;

my $debug = 0;

my $out_header = join("\t", "sample", "geneA", "chrA", "posA", "ortA", "featureA", "geneB", "chrB", "posB", "ortB", "featureB",
Expand Down Expand Up @@ -257,20 +259,16 @@
}

sub is_bad_fusion{
my $badfusion_distance_cutoff = 200;
my ($chrA, $posA, $chrB, $posB) = @_;
$chrA = "chr".$chrA unless($chrA =~ /chr/);
$chrB = "chr".$chrB unless($chrB =~ /chr/);
#print STDERR " test |".$chrA.":".$posA.":".$chrB.":".$posB."\n";
my $size = keys %bad_fusions;
#print STDERR " size |".$size."\n";
foreach my $xx (keys %bad_fusions) {
my ($chr1, $pos1, $chr2, $pos2) = split(":",$xx);
#print STDERR " badfusionlist |".$chr1.":".$pos1.":".$chr2.":".$pos2."\n";
return 1 if($chrA eq $chr1 && $chrB eq $chr2 &&
abs($pos1 - $posA) <$badfusion_distance_cutoff && abs($pos2 - $posB) <$badfusion_distance_cutoff);# cutoff is based on the cutoff of merging GTEx false positive fusions from CICERO running
abs($pos1 - $posA) < BADFUSION_DISTANCE_CUTOFF && abs($pos2 - $posB) < BADFUSION_DISTANCE_CUTOFF);# cutoff is based on the cutoff of merging GTEx false positive fusions from CICERO running
return 1 if($chrA eq $chr2 && $chrB eq $chr1 &&
abs($pos2 - $posA) <$badfusion_distance_cutoff && abs($pos1 - $posB) <$badfusion_distance_cutoff);
abs($pos2 - $posA) < BADFUSION_DISTANCE_CUTOFF && abs($pos1 - $posB) < BADFUSION_DISTANCE_CUTOFF);
}
return 0;
}
Expand Down Expand Up @@ -414,7 +412,7 @@ sub is_bad_fusion{
$second_bp->{tname} = normalizeChromosomeName($seq_ids[0], $second_bp->{tname});

# Ensure that the breakpoint chromosome names match
if(!$internal) {next if(is_bad_fusion($first_bp->{tname}, $first_bp->{tpos}, $second_bp->{tname}, $second_bp->{tpos}));}
next if(!$internal && is_bad_fusion($first_bp->{tname}, $first_bp->{tpos}, $second_bp->{tname}, $second_bp->{tpos}));

# Determine the variant type: CTX, Internal_inv, Interal_splicing, Internal_dup, ITX, read_through, DEL, INS
my $type = get_type($first_bp, $second_bp, $same_gene);
Expand Down Expand Up @@ -811,34 +809,6 @@ sub exist_multiplename_pair_checking {
return 0;
}

sub is_knownfusiongenepair{
my @genes1_tmp = %{(shift)};
my @genes2_tmp = %{(shift)};

foreach my $g1 (@genes1_tmp) {
foreach my $g2 (@genes2_tmp) {
return 1 if (exists($known_fusion_partners{$g1}{$g2}));
}
}

return 0;
}



sub exist_multiplename_checking {
my %genelist = %{(shift)};
my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
my @genes = split(/,|\|/, $targetgene);

foreach my $g1 (@genes) {
return 1 if(exists($genelist{$g1}));
}

return 0;
}


sub is_good_ITD {
my($bp1, $bp2) = @_;
my @genes = split(/,|\|/, $bp1->{gene});
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15 changes: 1 addition & 14 deletions src/scripts/get_geneInfo.pl
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Expand Up @@ -18,7 +18,7 @@
use lib dirname($0);
my $script_dir = dirname($0);
#custom packages
use CiceroUtil qw(parse_range is_PCR_dup);
use CiceroUtil qw(parse_range is_PCR_dup exist_multiplename_checking);
use TdtConfig;

use constant FQ_BASE_NUMBER => 33;
Expand Down Expand Up @@ -172,19 +172,6 @@ sub is_bad_chrom{
return 0;
}

sub exist_multiplename_checking {
my %genelist = %{(shift)};
my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
my @genes = split(/,|\|/, $targetgene);

foreach my $g1 (@genes) {
return 1 if(exists($genelist{$g1}));
}

return 0;
}


=head1 LICENCE AND COPYRIGHT
Copyright 2019 St. Jude Children's Research Hospital
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29 changes: 9 additions & 20 deletions src/scripts/rank_SVs.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
use List::Util qw[min max];
use TdtConfig;

use CiceroUtil qw(exist_multiplename_checking)

use DelimitedFile;
use File::Temp qw/ tempdir /;

Expand Down Expand Up @@ -299,15 +301,15 @@ sub scoring {
my $rating = 'LQ';

$medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg1));
$medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq "?");
$medal = 2 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq ">");
$medal = 3 if(exist_multiplename_checking(\%known_fusion_partners,$fg1) && exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{type} !~ /Internal/);
$medal = 4 if(exists_knownfusionlist_checking(\%known_fusions,$fg1,$fg2));
$medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq "?");
$medal = 2 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq ">");
$medal = 3 if(exist_multiplename_checking(\%known_fusion_partners,$fg1) && exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{type} !~ /Internal/);
$medal = 4 if(exists_knownfusionlist_checking(\%known_fusions,$fg1,$fg2));

my ($Is_known_ITD, $ITD_left_coor, $ITD_rightt_coor)=match_known_ITD(\%known_ITDs,$fg1);
my ($Is_known_ITD, $ITD_left_coor, $ITD_right_coor)=match_known_ITD(\%known_ITDs,$fg1);
if($Is_known_ITD && $type eq 'Internal_dup' &&
($bp1->{tpos} >= $ITD_left_coor) && ($bp1->{tpos} <= $ITD_rightt_coor) &&
($bp2->{tpos} >= $ITD_left_coor) && ($bp2->{tpos} <= $ITD_rightt_coor)){
($bp1->{tpos} >= $ITD_left_coor) && ($bp1->{tpos} <= $ITD_right_coor) &&
($bp2->{tpos} >= $ITD_left_coor) && ($bp2->{tpos} <= $ITD_right_coor)){
$rating = 'HQ'; $medal = 4;
}

Expand Down Expand Up @@ -366,7 +368,6 @@ sub is_dup_SV {
}

sub exists_knownfusionlist_checking {
my %genelist = %{(shift)};
my $targetgene1 = shift;#e.g. targetgene UBTF,MIR6782
my $targetgene2 = shift;#e.g. targetgene UBTF,MIR6782
my @genes1 = split(/,|\|/, $targetgene1);
Expand All @@ -382,18 +383,6 @@ sub exists_knownfusionlist_checking {
return 0;
}

sub exist_multiplename_checking {
my %genelist = %{(shift)};
my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
my @genes = split(/,|\|/, $targetgene);

foreach my $g1 (@genes) {
return 1 if(exists($known_fusion_partners{$g1}));
}

return 0;
}

sub match_known_ITD {
my %knownITDlist = %{(shift)};
my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
Expand Down

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