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circos.pipeline.pl
2020 lines (2014 loc) · 50.6 KB
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circos.pipeline.pl
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#!/usr/bin/perl -w
use strict;
use warnings;
my $BEGIN_TIME=time();
use Getopt::Long;
my ($snp,$indel,$sv,$cnv,$chrlist,$gff,$outdir,$paralist,$ssr,$snpplusindel,$outfile,$chromosome);
use Data::Dumper;
use FindBin qw($Bin $Script);
use File::Basename qw(basename dirname);
use List::Util qw(max min);
my $version="1.1.0";
GetOptions(
"help|?" =>\&USAGE,
"gff:s"=>\$gff,
"chrlist:s"=>\$chrlist,
"outdir:s"=>\$outdir,
"paramlist:s"=>\$paralist,
"outfile:s"=>\$outfile,
"chrom:s"=>\$chromosome,
) or &USAGE;
&USAGE unless ($gff and $chrlist and $paralist);
#$plottype||="line scatter histogram heatmap";#stuckbar
$gff=ABSOLUTE_DIR($gff);
$chrlist=ABSOLUTE_DIR($chrlist);
$outfile||="circos";
$outdir||="./";
########
########work dir
########
my $mkdir=1;
$mkdir=(mkdir "$outdir") if (!-d "$outdir");
$outdir=ABSOLUTE_DIR($outdir);
die "Error make dir $outdir" if ($mkdir == 0);
$mkdir=(mkdir "$outdir/draw.circos") if (!-d "$outdir/draw.circos");
die "Error make dir $outdir/draw.circos" if ($mkdir == 0);
$mkdir=(mkdir "$outdir/draw.circos/windows.file") if (!-d "$outdir/draw.circos/windows.file");
die "Error make dir $outdir/draw.circos/windows.file" if ($mkdir == 0);
open MC,">","$outdir/draw.circos/draw.conf";
open IDEO,">","$outdir/draw.circos/ideogram.conf";
open TIC,">","$outdir/draw.circos/ticks.conf";
open IM,">","$outdir/draw.circos/chromosomes.and.color.conf";
open HS,">","$outdir/draw.circos/housekeeping.conf";
my ($main_conf,$ideogram,$ticks,$chro,$housekeeping);
########
########chr and band file
########
open CHR,$chrlist;
open GFF,$gff;
open CHRBAND,">$outdir/draw.circos/chr.band.txt";
my %hash_chr_length;
my %hash_gff;
my %hash_chr_num;
my $chr_type;
while(<CHR>){
#$_=~s/sca//g;
$_=~s/[\n\r]//g;
next if ($_ eq ""||/^$/||/^#/);
my ($chr,$length)=split;
if ($chr =~ /chr/) {
$chr_type="chr";
}else{
$chr_type="sca";
}
$hash_chr_num{$chr}=1;
$hash_chr_length{$chr}=$length;
}
my $chrnum=scalar keys %hash_chr_num;
#open OUTT,">win.number.txt";
my $gff_windows=100000;
while(<GFF>){
next if /^#/;
$_=~s/[\n\r]//g;
my ($chr,undef,$type,$start,@others)=split(/\t/,$_);
my $win_num=int($start/$gff_windows)+1;
#print OUTT $win_num."\n";
if (exists $hash_chr_num{$chr} and ($type=~/gene/ || ($type !~ /CDS/ && $type !~/exon/)) ){
if ($chr =~ /chr/) {$chr=~s/chr//g;}
if ($chr =~ /sca/) {$chr=~s/sca//g;}
$hash_gff{$chr}{$win_num}++;
}
}
##draw colour of band
my %region;
my %bands;
open CO,">$outdir/draw.circos/band.txt";
my @chr_windows;
foreach my $keys (sort {$a<=>$b}keys %hash_gff){
my $band=1;
my $max=0;
foreach my $num (sort keys %{$hash_gff{$keys}}){
my $start=1+$gff_windows*($num-1);
my $end=$gff_windows*$num;
my $snp=$hash_gff{$keys}{$num}/$gff_windows;
$region{$chr_type}{join("\t",$start,$end)}=1;
push(@chr_windows,$snp);
if($max < $num){
$max=$num;
}
print CO "band\t$chr_type"."$keys\tband$band\tband$band\t$start\t$end\t$snp\n";
$band++;
}
my $bandnum=$keys;
$bandnum=~s/$chr_type//g;
print CHRBAND "chr"."\t"."-"."\t".$chr_type."".$keys."\t".$bandnum."\t"."0"."\t".$max*$gff_windows."\t".$chr_type."".$keys."\n";
}
close CO;
open BANDCOL,"<$outdir/draw.circos/band.txt";
my $band_windows=(max(@chr_windows)-min(@chr_windows))/10;
while(<BANDCOL>){
$_=~s/[\n\r]//g;
my @array=split;
my $win_num=int($array[6]/$band_windows)+1;
$array[5]=$array[5]-1;
print CHRBAND "$array[0]\t$array[1]\t$array[2]\t$array[3]\t$array[4]\t$array[5]\tbandcol$win_num\n";
# print CHRBAND join("\t",@array[1..($#array-1)])."\t"."bandcol".$win_num."\n";
}
close CHR;
close GFF;
close CHRBAND;
########
########
########
#my $drawchr=join("",(1..$chrnum));
my @draw_chr=sort {$hash_chr_num{$a} <=> $hash_chr_num{$b}} keys %hash_chr_num;
my $chr_draw=join(";",@draw_chr);
if ($chromosome){
my $chroms=join(";",split(",",$chromosome));
$chro.="
chromosomes_units = 1000000
chromosomes_display_default = no
chromosomes=$chroms #chromosomes = hs1:(-100,120-);hs2;hs3;h4
#chromosomes_order =$chr_draw
<colors>
";
}else{
$chro.="
chromosomes_units = 1000000
chromosomes_display_default = yes
chromosomes=$chr_draw #chromosomes = hs1:(-100,120-);hs2;hs3;h4
#chromosomes_order =$chr_draw
<colors>
";
}
my %chr_colour;
my $num;
for(my $i=0;$i<@draw_chr;$i++){
my $num=$i%6;
#print $num;
if($i%6==0){
$chro.="$draw_chr[$i]* = col6\n";
$chr_colour{$draw_chr[$i]}="col6";
}
else{
$chro.="$draw_chr[$i]* = col$num\n";
$chr_colour{$draw_chr[$i]}="col".$num;
}
}
$chro.="
</colors>
";
#print $num\t$chr_draw;die;
#########
#########
#########
if (-e "$outdir/draw.circos/chr.band.txt"){
$main_conf.="
karyotype = $outdir/draw.circos/chr.band.txt
<<include $outdir/draw.circos/ideogram.conf>>
<<include $outdir/draw.circos/ticks.conf>>
<<include $outdir/draw.circos/chromosomes.and.color.conf>>
<image>
<<include etc/image.conf>>
radius* = 2000
</image>
";
}
########
########
########
$ideogram="
<ideogram>
<spacing>
default = 0.005r
</spacing>
radius = 0.9r
thickness = 100p
fill = yes
fill_color = black
#stroke_thickness = 2
#stroke_color = black
show_label = yes
label_font = default
label_radius = 1r + 75p
label_size = 30
label_parallel = yes
label_case = lower#upper
label_format = eval(sprintf(\"$chr_type%s\",var(label)))
show_bands = yes
fill_bands = yes
band_stroke_thickness = 1
band_stroke_color = black
band_transparency = 2
#label_with_tag = no
</ideogram>
";
#########
#########
#########
$ticks="
show_ticks = no
show_tick_labels = no
<ticks>
radius = 1r
color = black
thickness = 2p
multiplier = 1e-6
format = %d
<tick>
spacing = 5u
size = 10p
</tick>
<tick>
spacing = 25u
size = 15p
show_label = yes
label_size = 20p
label_offset = 10p
format = %d
</tick>
</ticks>
";
$housekeeping.="
anglestep = 0.5
minslicestep = 10
beziersamples = 40
debug = no
warnings = no
imagemap = no
paranoid = no
units_ok = bupr
units_nounit = n
file_delim = \\s
file_delim_collapse = yes
list_record_delim = \\s*[;,]\\s*
list_field_delim = \\s*[:=]\\s*
options_record_delim = [,;]
options_field_delim = =
skip_missing_expression_vars = no
legacy_underline_expression_syntax = no
svg_font_scale = 1.3
sup_baseline_shift = 40
sub_baseline_shift = -40
sup_fontsize = 90
sub_fontsize = 90
default_font = default
default_font_name = Arial
default_font_color = black
default_color = black
<guides>
thickness = 1
size = 5
type = outline
<object>
all = no
ideogram = no
ideogram_label = no
</object>
<color>
default = lblue
text = red
</color>
</guides>
debug_group = summary,output
debug_auto_timer_report = 3600
debug_word_separator = \" \"
debug_undef_text = _undef_
debug_empty_text = _emptylist_
debug_validate = yes
debug_output_tidy = no
text_pixel_subsampling = 1
text_snuggle_method = array
restrict_parameter_names = no
case_sensitive_parameter_names = no
calculate_track_statistics = yes
color_cache_static = yes
color_cache_file = circos.colorlist
color_lists_use = yes
memoize = yes
quit_on_dump = yes
offsets = 0,0
max_ticks = 5000
max_ideograms = 200
max_links = 25000000000000000000
max_points_per_track = 25000000000000000000
undefined_ideogram = skip
relative_scale_iterations = 10
relative_scale_spacing = mode
data_out_of_range = trim,warn
track_defaults = etc/tracks
round_brush_use = yes
round_brush_min_thickness = 5
anti_aliasing = yes
housekeeping = yes
auto_eval = no
";
#########
$main_conf.="
<plots>
<backgrounds>
show = data
<background>
color = vvlgrey
y0 = 1.0r
y1 = 0r
</background>
</backgrounds>
";
open PA,$paralist;
my @para;
my $nlm=1;
while (<PA>) {
chomp;
next if ($_=~ "#");
@para=split/\s+/,$_;
my($r1,$r0)=split/\,/,$para[2];
#print "$para[3]\t$para[5]";die;
if($para[3] eq "snp" && $para[5] ne "NA"){######plot snp
open In,$para[7];
if ($para[7]=~/.gz$/) {
close In;
open In,"gunzip -c $snp|";
}
my $nsam;
my @sample;
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
while(<In>){
chomp;
next if(/^##/);
if (/^#/){
my (undef,undef,undef,undef,undef,undef,undef,undef,undef,@sample)=split/\s+/,$_;
#print Dumper @sample;
my $sam=9;
for(my $i=0;$i<@sample;$i++){
if ($para[5] eq $sample[$i]){
$nsam=$sam+$i;
last;
}else{
next;
}
}
}
next if(/^#/);
my @array=split;
my ($gt,undef)=split/\:/,$array[$nsam],2;
next if ($gt eq "./.");
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
#my $file_name=$para[5];
open OUT,">$outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt";
foreach my $keys (sort keys %hash){
# print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $snp=$hash{$keys}{$num}/$win;
$hash_max{$snp}=1;
print OUT "$chr\t$start\t$end\t$snp\tfill_color=$chr_colour{$chr}\n";
}
}
#print \%hash_max;die;
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
##if line or heatmap
if ($para[4] eq "line"){
$main_conf.="
######plot snp
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot snp
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot snp
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot snp
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif($para[3] eq "snp" && $para[5] eq "NA"){
open In,$para[7];
if ($para[7]=~/.gz$/) {
close In;
open In,"gunzip -c $snp|";
}
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
#open OUT,">$out";
while(<In>){
#$_=~s/sca/chr/g;
next if (/^#/);
#$_=~s/[\n\r]//g;
#print $_;
my @array=split;
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
}
close In;
#my $file_name=(split/\//,$snp)[-1];
open OUT,">$outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt";
foreach my $keys (sort keys %hash){
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $snp=$hash{$keys}{$num}/$win;
$hash_max{$snp}=1;
print OUT "$chr\t$start\t$end\t$snp\tfill_color=$chr_colour{$chr}\n";
}
}
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
##if line or heatmap
if ($para[4] eq "line"){
$main_conf.="
######plot snp
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot snp
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot snp
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot snp
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/$para[5].snp.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif($para[3] eq "indel" && $para[5] ne "NA"){######plot indel
#print $para[5];die;
my $nsam;
my @sample;
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
open In,$para[7];
while(<In>){
chomp;
next if(/^##/);
#my $nsam;
if (/^#/){
#print "$_";die;
my (undef,undef,undef,undef,undef,undef,undef,undef,undef,@sample)=split/\s+/,$_;
#print Dumper @sample;
my $sam=9;
for(my $i=0;$i<@sample;$i++){
if ($para[5] eq $sample[$i]){
#print $sample[$i];
$nsam=$sam+$i;
#print $nsam;
last;
}else{
next;
}
}
}
next if(/^#/);
my @array=split;
my ($gt,undef)=split/\:/,$array[$nsam],2;
next if ($gt eq "./.");
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
open OUT,">$outdir/draw.circos/windows.file/$para[5].indel.$nlm.win.txt";
foreach my $keys (sort keys %hash){
# print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $indel=$hash{$keys}{$num}/$win;
$hash_max{$indel}=1;
print OUT "$chr\t$start\t$end\t$indel\tfill_color=$chr_colour{$chr}\n";
}
}
#print \%hash_max;die;
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
if ($para[4] eq "line"){
$main_conf.="
######plot indel
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/$para[5].indel.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot indel
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/$para[5].indel.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot indel
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/$para[5].indel.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot indel
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/$para[5].indel.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif($para[3] eq "indel" && $para[5] eq "NA"){
open In,$para[7];
if ($para[7]=~/.gz$/) {
close In;
open In,"gunzip -c $indel|";
}
my $max;
my %hash;
my $win=$para[6] ;
my %hash_max;
#open OUT,">$out";
while(<In>){
#$_=~s/sca/chr/g;
next if (/^#/);
#$_=~s/[\n\r]//g;
#print $_;
my @array=split;
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
open OUT,">$outdir/draw.circos/windows.file/indel.$nlm.win.txt";
foreach my $keys (sort keys %hash){
# print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $indel=$hash{$keys}{$num}/$win;
$hash_max{$indel}=1;
print OUT "$chr\t$start\t$end\t$indel\tfill_color=$chr_colour{$chr}\n";
}
}
#print \%hash_max;die;
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
if ($para[4] eq "line"){
$main_conf.="
######plot indel
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/indel.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot indel
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/indel.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot indel
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/indel.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot indel
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/indel.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif ($para[3] eq "snpplusindel" && $para[5] ne "NA"){######plot $snpplusindel
my $nsam;
my @sample;
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
open In,$para[7];
if ($para[7]=~/.gz$/) {
close In;
open In,"gunzip -c $snpplusindel|";
}
while(<In>){
chomp;
next if(/^##/);
#my $nsam;
if (/^#/){
#print "$_";die;
my (undef,undef,undef,undef,undef,undef,undef,undef,undef,@sample)=split/\s+/,$_;
#print Dumper @sample;
my $sam=9;
for(my $i=0;$i<@sample;$i++){
if ($para[5] eq $sample[$i]){
#print $sample[$i];
$nsam=$sam+$i;
#print $nsam;
last;
}else{
next;
}
}
}
next if(/^#/);
my @array=split;
my ($gt,undef)=split/\:/,$array[$nsam],2;
next if ($gt eq "./.");
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
open OUT,">$outdir/draw.circos/windows.file/$para[5].snpplusindel.$nlm.win.txt";
foreach my $keys (sort keys %hash){
# print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $snpplusindel=$hash{$keys}{$num}/$win;
$hash_max{$snpplusindel}=1;
print OUT "$chr\t$start\t$end\t$snpplusindel\tfill_color=$chr_colour{$chr}\n";
}
}
#print \%hash_max;die;
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
if ($para[4] eq "line"){
$main_conf.="
######plot indel
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/$para[5].snpplusindel.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot indel
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/$para[5].snpplusindel.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot indel
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/$para[5].snpplusindel.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot indel
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/$para[5].snpplusindel.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif($para[3] eq "snpplusindel" && $para[5] eq "NA"){
open In,$para[7];
if ($para[7]=~/.gz$/) {
close In;
open In,"gunzip -c $snpplusindel|";
}
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
#open OUT,">$out";
while(<In>){
#$_=~s/sca/chr/g;
next if (/^#/);
#$_=~s/[\n\r]//g;
#print $_;
my @array=split;
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
open OUT,">$outdir/draw.circos/windows.file/snpplusindel.$nlm.win.txt";
foreach my $keys (sort keys %hash){
#print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;
my $snpplusindel=$hash{$keys}{$num}/$win;
$hash_max{$snpplusindel}=1;
print OUT "$chr\t$start\t$end\t$snpplusindel\tfill_color=$chr_colour{$chr}\n";
}
}
#print \%hash_max;die;
$max= (sort{$b<=>$a} keys %hash_max)[0];
#print $max;
close OUT;
if ($para[4] eq "line"){
$main_conf.="
######plot indel
<plot>
type = line
max_gap = 1u
file = $outdir/draw.circos/windows.file/snpplusindel.$nlm.win.txt
color = white
min = 0
max = $max#0.015
r1 = $r1
r0 = $r0
thickness = 1
#fill_color = vdyellow
</plot>
######
";
}elsif($para[4] eq "scatter"){
$main_conf.="
######plot indel
<plot>
type=scatter
file = $outdir/draw.circos/windows.file/snpplusindel.$nlm.win.txt
#fill_color=green
stroke_color=blue
glyph=circle#rectangle
glyph_size=10
max=$max#0.013
min=0
r1 = $r1
r0 = $r0
</plot>
######
";
}elsif($para[4] eq "heatmap"){
$main_conf.="
######plot indel
<plot>
type=heatmap
file = $outdir/draw.circos/windows.file/snpplusindel.$nlm.win.txt
color = col1,col2,col3,col4,col5
r1 = $r1
r0 = $r0
</plot>
######
";
}else{
$main_conf.="
######plot indel
<plot>
type=histogram
file = $outdir/draw.circos/windows.file/snpplusindel.$nlm.win.txt
color = white
r1 = $r1
r0 = $r0
#orientation = out
</plot>
######
";
}
}elsif($para[3] eq "cnv" && $para[5] ne "NA"){######plot cnv both same format
open In,$para[7];
my $max;
my %hash;
my $win=$para[6];
my %hash_max;
while(<In>){
#$_=~s/sca/chr/g;
next if (/^#/);
#$_=~s/[\n\r]//g;
#print $_;
my @array=split;
my $win_num=int($array[1]/$win)+1;
next if (!exists $hash_chr_num{$array[0]});
$hash{$array[0]}{$win_num}++;
#print Dumper \%hash;die;
}
close In;
open OUT,">$outdir/draw.circos/windows.file/$para[5].$nlm.cnv.txt";
foreach my $keys (sort keys %hash){
#print "$keys\n";
foreach my $num (sort keys %{$hash{$keys}}){
my $chr=$keys;
my $start=1+$win*($num-1);
my $end=$win*$num;