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combine_call.pl
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combine_call.pl
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#!/usr/bin/perl
use strict;
use warnings;
die "Usage perl combine_call.pl SAMPLE STARFUSION ERICSCRIPT INTEGRATE_summary INTEGRATE_breakpoint OUTDIR\nFilterDB and STARDB are set to be static in the script\n" if (@ARGV < 1);
my $filterDB = "/storage1/fs1/dinglab/Active/Projects/PECGS/PECGS_pipeline/Fusion/FilterDatabase";
open(IN, "$filterDB/hgnc_complete_set.txt");
#different names for the same gene
<IN>;
my %hash;
while(<IN>)
{
chomp;
my @l=split(/\t/,);
$hash{$l[1]}=$l[0];
if($l[10] ne "")
{
$l[10]=~s/\"//g;
my @m=split(/\|/,$l[10]);
foreach my $g (@m)
{
$hash{$g}=$l[0];
}
}
}
my $sample = $ARGV[0];
my $star = $ARGV[1];
my (@names, $cancer, %mark, %star, %integrate, %eric, %gtex);
open(IN, "$star");
<IN>;
while(<IN>)
{
chomp;
my @l = split(/\t/,);
my $id = $l[0];
if($_=~m/GTEx_Recurrent/)
{
$gtex{$l[0]} = 1;
}
$star{$id} = "$l[0]\t$l[5]\t$l[7]\t$sample\t$l[1]\t$l[2]\t$l[13]\t$l[19]";
my @m = split(/\-\-/, $l[0]);
if(exists $hash{$m[0]})
{
$mark{$hash{$m[0]}}=$m[0];
}
if(exists $hash{$m[1]})
{
$mark{$hash{$m[1]}}=$m[1];
}
#always use the names in STAR-Fusion
}
my $eric = $ARGV[2];
open(IN, "$eric");
<IN>;
while(<IN>)
{
chomp;
my @l=split(/\t/,);
my $a=(exists $hash{$l[0]} && exists $mark{$hash{$l[0]}}) ? $mark{$hash{$l[0]}} : $l[0];
my $b=(exists $hash{$l[1]} && exists $mark{$hash{$l[1]}}) ? $mark{$hash{$l[1]}} : $l[1];
if($l[3]=~m/Unable/)
{
$l[3]="Unable";
}
if($l[6]=~m/Unable/)
{
$l[6]="Unable";
}
my $id = $a."\-\-".$b;
$eric{$id} = "$a\-\-$b\tchr$l[2]\:$l[3]\:$l[4]\tchr$l[5]\:$l[6]\:$l[7]\t$sample\t$l[10]\t$l[11]";
}
my $integrate_summary = $ARGV[3];
my $integrate_breakpoint = $ARGV[4];
open(IN, "$integrate_summary");
<IN>;
open(IN2, "$integrate_breakpoint");
<IN2>;
while(<IN>)
{
chomp;
my @l=split(/\t/,);
my $match=<IN2>;
chomp $match;
my @ll = split(/\t/,$match);
my $a=(exists $hash{$l[1]} && exists $mark{$hash{$l[1]}}) ? $mark{$hash{$l[1]}} : $l[1];
my $b=(exists $hash{$l[2]} && exists $mark{$hash{$l[2]}}) ? $mark{$hash{$l[2]}} : $l[2];
my $id = $a."\-\-".$b;
$integrate{$id} = "$a\-\-$b\tchr$ll[2]\:$ll[4]\:+\tchr$ll[5]\:$ll[7]\:+\t$sample\t$l[6]\t$l[7]";
#strand info will be corrected using EricScript
}
my $outdir = $ARGV[5];
open(OUT1, ">$outdir/Total_Fusions_in_$sample.tsv");
open(OUT3, ">$outdir/STARFusion_not.tsv");
print OUT1 "FusionName\tLeftBreakpoint\tRightBreakpoint\tSample\tJunctionReadCount\tSpanningFragCount\tFFPM\tPROT_FUSION_TYPE\tGTEx\tCallerN\n";
print OUT3 "#FusionName\tJunctionReadCount\tSpanningFragCount\tSpliceType\tLeftGene\tLeftBreakpoint\tRightGene\tRightBreakpoint\tLargeAnchorSupport\tLeftBreakDinuc\tLeftBreakEntropy\tRightBreakDinuc\tRightBreakEntropy\tFFPM\n";
#my $stardb = "/storage1/fs1/dinglab/Active/Projects/PECGS/PECGS_pipeline/Fusion/STAR-Fusion_dependencies/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir";
my $stardb = "/storage1/fs1/dinglab/Active/Projects/PECGS/PECGS_pipeline/Fusion/STAR-Fusion_dependencies/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir";
open(REF, "$stardb/ref_annot.gtf");
my %refdb;
my %transname;
while(<REF>)
{
chomp;
my $id;
next if $_=~m/^#/;
my @l = split(/\t/,);
if($l[2] eq "gene")
{
my @a=split(/\"/,$l[8]);
$transname{$a[9]}=$a[1];
#GRC37 and 38 have different formats
}elsif($l[2] eq "exon")
{
$id=$l[0].":".$l[3].":".$l[6];
$refdb{$id}="";
$id=$l[0].":".$l[4].":".$l[6];
$refdb{$id}="";
}
}
my @tmp_sample;
foreach my $g (keys %eric)
{
my $beforeformat;
if(exists $integrate{$g} && !exists $star{$g})
{
if($eric{$g}=~m/Unable/)
{
my @e = split(/\t/,$eric{$g});
my @i = split(/\t/,$integrate{$g});
my ($b1, $b2);
if($e[1]=~m/Unable/)
{
my @a=split(/\:/,$e[1]);
my @b=split(/\:/,$i[1]);
$b1=join("\:",$a[0],$b[1],$a[2]);
}else
{
$b1=$e[1];
}
if($e[2]=~m/Unable/)
{
my @a=split(/\:/,$e[2]);
my @b=split(/\:/,$i[2]);
$b2=join("\:",$a[0],$b[1],$a[2]);
}else
{
$b2=$e[2];
}
$beforeformat = "$e[0]\t$b1\t$b2\t$e[3]\t$e[4]\t$e[5]";
}else
{
$beforeformat = "$eric{$g}";
}
my @before = split(/\t/,$beforeformat);
my @m = split(/\-\-/,$before[0]);
if($m[0] eq "PPP2R4")
{
$m[0] = "PTPA";
}
#one case with different names
my $type=(exists $refdb{$before[1]} && exists $refdb{$before[2]}) ? "ONLY_REF_SPLICE" : "INCL_NON_REF_SPLICE";
print OUT3 "$before[0]\t$before[4]\t$before[5]\t$type\t$m[0]\^$transname{$m[0]}\t$before[1]\t$m[1]\^$transname{$m[1]}\t$before[2]\tYES_LDAS\tGT\t1\tAG\t1\t0.1\n";
push @tmp_sample, $before[3];
}
}
my $annodir = "/storage1/fs1/dinglab/Active/Projects/PECGS/PECGS_pipeline/Fusion/FusionAnnotator";
my $new_annot = `$annodir/FusionAnnotator --genome_lib_dir $stardb --annotate $outdir/STARFusion_not.tsv | $annodir/util/fusion_to_coding_region_effect.pl --fusions - --genome_lib_dir $stardb`;
my @lines = split(/\n/, $new_annot);
shift @lines;
for(my $i=0; $i<=$#lines; $i++)
{
my @after = split(/\t/,$lines[$i]);
if($lines[$i]=~m/GTEx_Recurrent/)
{
$gtex{$after[0]} = 1;
}
}
foreach my $g (keys %star)
{
my @l = split(/\t/,$star{$g});
my $val = (exists $gtex{$l[0]}) ? 1 : 0;
if(exists $integrate{$g})
{
if(exists $eric{$g})
{
print OUT1 "$star{$g}\t$val\t3\n";
}else
{
print OUT1 "$star{$g}\t$val\t2\n";
}
}else
{
if(exists $eric{$g})
{
print OUT1 "$star{$g}\t$val\t2\n";
}else
{
print OUT1 "$star{$g}\t$val\t1\n";
}
}
}
for(my $i=0; $i<=$#lines; $i++)
{
my @after = split(/\t/,$lines[$i]);
my $val = (exists $gtex{$after[0]}) ? 1 : 0;
print OUT1 "$after[0]\t$after[5]\t$after[7]\t$tmp_sample[$i]\t$after[1]\t$after[2]\tNA\t$after[19]\t$val\t2\n";
}
system("rm -f $outdir/STARFusion_not.tsv");