From 2089653300a689c95fb6e9f94f967dd36ca3d141 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 8 May 2019 14:09:25 -0500
Subject: [PATCH] minding my ps and qs
---
variants/filter_cnvkit.pl | 26 +++++++++++++++++---------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index b4ddacc..188b7f5 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -36,7 +36,8 @@ while (my $line = <CYTO>) {
my ($chrom,$start,$end,$band) = split(/\t/,$line);
my $key = $chrom.":".$start."-".$end;
$band =~ m/^(\w)(.+)/;
- push @{$cyto{$key}}, [$1,$2];
+ next unless ($1 && $2);
+ push @{$cyto{$key}{$1}},$2;
}
open OUT, ">$prefix\.cnvcalls.txt" or die $!;
@@ -115,16 +116,23 @@ while (my $line = <IN>) {
$cn_cbio = 2 if ($cn > 4);
print BIO join("\t",$gene,$entrez{$gene},$cn_cbio),"\n";
print BIO2 join("\t",$gene,$entrez{$gene},$log2),"\n";
- my @cytoband = sort {$a->[1] <=>$b->[1]} @{$cyto{$key}};
- if (join("",@{$cytoband[0]}) eq join("",@{$cytoband[-1]})) {
- $cband = join("",@{$cytoband[0]});
+ my @cytoband;
+ if (@{$cyto{$key}{'p'}}) {
+ @nums = sort {$b <=> $a} @{$cyto{$key}{'p'}};
+ push @cytoband, 'p'.$nums[0],'p'.$nums[-1];
+ } if (@{$cyto{$key}{'q'}}) {
+ @nums = sort {$a <=> $b} @{$cyto{$key}{'q'}};
+ push @cytoband, 'q'.$nums[0],'q'.$nums[-1];
+ }
+ if ($cytoband[0] eq $cytoband[-1]) {
+ $cband = $cytoband[0];
}else {
- $cband = join("",@{$cytoband[0]},'-',@{$cytoband[-1]});
+ $cband = join("-",$cytoband[0],$cytoband[-1]);
}
- print OUT2 join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight,$cband),"\n";
- print OUT join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight),"\n";
- }
-}
+ print OUT2 join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight,$cband),"\n";
+ print OUT join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight),"\n";
+ }
+ }
close IN;
close OUT;
close BIO;
--
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