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prepare.data.pl
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prepare.data.pl
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#!/usr/bin/env perl -w
#use strict;
use warnings;
use Getopt::Long;
use List::Util qw(max min);
use FindBin qw($Bin);
use lib "$Bin";
use myth qw(format_scale read_list draw_genes display_conf read_conf default_setting check_track_order check_para get_para);
my ($list,$prefix,$outdir,$conf, $confile, $track_reorder);
GetOptions("list:s"=>\$list,
"prefix:s"=>\$prefix,
"outdir:s"=>\$outdir,
"conf:s"=>\$confile
);
die "
perl $0 [options]:
* --list <str> two formats: [sample gff genome seq_id1 seq_draw_start1 seq_draw_end1 genome seq_id2 seq_draw_start2 seq_draw_end2 ...]
or [sample gff genome]no seq_id mean full length of whole gff
* --prefix <str>
* --outdir <str>
* --conf <str>
writed by myth
" unless($list && $prefix && $outdir && $confile);
if(! -d "$outdir"){
`mkdir -p $outdir`;
}
my @track_reorder;
my @funcs=("hist_scatter_line", "reads_mapping", "synteny");
my %conf = &read_conf($confile, @funcs);
($conf, $track_reorder) = &default_setting(%conf);
%conf=%$conf;
@track_reorder=@$track_reorder;
&check_para(%conf);
###start:get scaffold length in genome file and scaffold length in gff file of list
my ($genome, $gff, $track_order, $sample_num, $fts) = &read_list($list, \%conf);
my %genome=%$genome;
my %gff=%$gff;
my %fts=%$fts;
my @track_order=@$track_order;
for my $fun (@funcs){
&$fun(\%gff, \%conf);
}
print "\ndata done\n";
sub synteny(){
my ($gff, $conf)=@_;
my $ex="synteny=order->1,query->s1:target->s2,../data/s1.mapto.s2.paf.gz,paf,quadrilateral,forward->yellow->opacity1,reverse->blue->opacity1,cross_link_shift_y->+1:-1,sort->1";
unless(exists $conf->{synteny} && $conf->{synteny}){
print "synteny not\n";
return 0;
}
print "synteny start\n";
my $k_index;
my (%outname);
my @show_types=("quadrilateral");
#my @highs=("highlight_vlines", "start_end_xaxis","color_height_cs", "display_feature_label", "feature_x_extent","ylabel");
my @highs=("blat_block_show");
my @align_types=("paf", "blast_m8", "blat_psl", "mummer_coords");
for my $k (@{$conf->{synteny}}){
$k_index++;
&check_highs(\@highs,$k);
print "$k_index is $k\n\n";
my @ks = split(/\t+/, $k);
my @infos=split(/,/, $ks[0]);
my $infos_len=scalar(@infos);
if($infos_len != 9 ){
die "\nerror: synteny should separate by \\t, and have 9 colums for synteny=$k, but only have $infos_len\nvalid like synteny=$ex\n";
}
my @arr=$ks[0]=~ /^order->(-?\d+),query->([^:]+):target->([^,]+),(\S+),(\S+),(\S+),forward->([^-]+)->opacity([\d\.]+),reverse->([^-]+)->opacity([\d\.]+),cross_link_shift_y->(\+[\d\.]+:-[\d\.]+),sort->([01])$/;
die "\nerror: $ks[0] format \nerror, should like $ex\n" if(@arr!=12);
my ($synteny_order,$query_name,$target_name,$alignment,$alignment_type,$crosslink_shape,$forward_color,$forward_opacity,$reverse_color,$reverse_opacity, $cross_link_shift_y,$sort) = @arr;
die "\nerror: not support $alignment_type, only support @align_types\n" if(! grep(/^$alignment_type$/, @align_types));
die "\nerror: not support $crosslink_shape, only support @show_types\n" if(! grep(/^$crosslink_shape$/, @show_types));
die "\nerror: $query_name not exists in --list\n" if(not exists $conf->{sample_scf}{$query_name});
die "\nerror: $target_name not exists in --list\n" if(not exists $conf->{sample_scf}{$target_name});
#$conf{sample_scf}{$sample}{$id}="";
my ($synteny_gff_q, $synteny_setting_conf_q, $synteny_gff_t, $synteny_setting_conf_t,$cross_link_conf)=&synteny_run(\@arr, $conf,$k_index, $k);
my $prefix="$query_name.$query_name.to.$target_name.$alignment_type.$crosslink_shape.$k_index.synteny";
%outname = &gather_gff_conf_link($prefix,$synteny_gff_q,$synteny_setting_conf_q,"", \%outname, $query_name);
$prefix="$target_name.$query_name.to.$target_name.$alignment_type.$crosslink_shape.$k_index.synteny";
%outname = &gather_gff_conf_link($prefix,$synteny_gff_t,$synteny_setting_conf_t,"", \%outname, $target_name);
$prefix="$query_name.to.$target_name.$alignment_type.$crosslink_shape.$k_index.synteny";
%outname = &gather_gff_conf_link($prefix,"","",$cross_link_conf, \%outname, "$query_name.to.$target_name");
}
&write_gff_conf_link(\%outname, "synteny");
}
sub synteny_run(){
my ($arr,$conf,$k_index, $k)=@_;
my ($synteny_order,$query_name,$target_name,$alignment,$alignment_type,$crosslink_shape,$forward_color,$forward_opacity,$reverse_color,$reverse_opacity, $cross_link_shift_y, $sort)=@$arr;
my ($synteny_gff_q, $synteny_setting_conf_q,$synteny_gff_t, $synteny_setting_conf_t, $cross_link_conf);
my (%qid, %tid, $qtid);
#my $feature_color="white";
my $cross_link_opacity;
my $cross_link_color;
my %align;
my @pairs;
if($alignment_type eq "paf"){
if($alignment=~ /\.paf$/){
if($sort){
open PAF,"cat $alignment|sort -k 10nr,10nr -k 1,1 -k 6,6|" or die "$?";
}else{
open PAF,"$alignment" or die "$?";
}
print "$alignment is plain file\n";
}elsif($alignment=~ /\.gz/){
if($sort){
open PAF,"gzip -dc $alignment|sort -k 10nr,10nr -k 1,1 -k 6,6|" or die "$?";
}else{
open PAF,"gzip -dc $alignment|" or die "$?";
}
print "$alignment is gz file\n";
}else{
die "\nerror:$alignment should end with paf or gz\n";
}
while(<PAF>){
chomp;
next if($_=~ /^#/ ||$_=~ /^\s*$/);
#print "line$. is $_\n";
my @arr=split(/\s+/,$_);
die "error:alignment sholud be >12 columns in $alignment\n" if(@arr<12);
my $query_scf=$arr[0];
my $target_scf=$arr[5];
my $query_start=($arr[2] ==0)? 1:$arr[2];
my $query_end=$arr[3];
my $target_start=($arr[7] ==0)? 1:$arr[7];
my $target_end=$arr[8];
my $strand=$arr[4];
die "\nerror:$query_scf of $query_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$query_name}{$query_scf});
die "\nerror:$target_scf of $target_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$target_name}{$target_scf});
my $query_feature_id="$query_name.$query_scf.$query_start.$query_end.$k_index.$strand";
my $target_feature_id="$target_name.$target_scf.$target_start.$target_end.$k_index.$strand";
my $query_target_feature_id="$query_feature_id -> $target_feature_id";
my $indentity=$arr[9]/$arr[10]*100;
my $q_cov=(1+abs($arr[2]-$arr[3]))/$arr[1] * 100;
my $t_cov=(1+abs($arr[7]-$arr[8]))/$arr[6] * 100;
$align{query}{$query_feature_id}{query_scf}=$query_scf;
$align{query}{$query_feature_id}{query_start}=$query_start;
$align{query}{$query_feature_id}{query_end}=$query_end;
$align{qt}{$query_target_feature_id}{strand}=$strand;
$align{qt}{$query_target_feature_id}{indentity}=$indentity;
$align{qt}{$query_target_feature_id}{q_cov}=$q_cov;
$align{qt}{$query_target_feature_id}{t_cov}=$t_cov;
$align{target}{$target_feature_id}{target_scf}=$target_scf;
$align{target}{$target_feature_id}{target_start}=$target_start;
$align{target}{$target_feature_id}{target_end}=$target_end;
push(@pairs,$query_target_feature_id);
}
close PAF;
}elsif($alignment_type eq "blast_m8"){
if($alignment=~ /\.gz/){
if($sort){
open BLAST,"gzip -dc $alignment|sort -k 4nr,4nr -k 1,1 -k 2,2|" or die "$?";
}else{
open BLAST,"gzip -dc $alignment|" or die "$?";
}
print "$alignment is gz file\n";
}else{
if($sort){
open BLAST,"cat $alignment|sort -k 4nr,4nr -k 1,1 -k 2,2|" or die "$?";
}else{
open BLAST,"$alignment" or die "$?";
}
print "$alignment is plain file\n";
}
while(<BLAST>){
chomp;
next if($_=~ /^#/ ||$_=~ /^\s*$/);
#print "line$. is $_\n";
my @arr=split(/\s+/,$_);
die "error:alignment sholud be 12 columns in $alignment\n" if(@arr!=12);
my $query_scf=$arr[0];
my $target_scf=$arr[1];
my $query_start=$arr[6];
my $query_end=$arr[7];
my $target_start=$arr[8];
my $target_end=$arr[9];
my $strand=($arr[9]>$arr[8])? "+":"-";
die "\nerror:$query_scf of $query_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$query_name}{$query_scf});
die "\nerror:$target_scf of $target_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$target_name}{$target_scf});
my $query_feature_id="$query_name.$query_scf.$query_start.$query_end.$k_index.$strand";
my $target_feature_id="$target_name.$target_scf.$target_start.$target_end.$k_index.$strand";
my $query_target_feature_id="$query_feature_id -> $target_feature_id";
my $indentity=$arr[2];
my $q_cov=(abs($arr[7]-$arr[6])+1)/$arr[3] * 100;
my $t_cov=(abs($arr[9]-$arr[8])+1)/$arr[3] * 100;
$align{query}{$query_feature_id}{query_scf}=$query_scf;
$align{query}{$query_feature_id}{query_start}=$query_start;
$align{query}{$query_feature_id}{query_end}=$query_end;
$align{qt}{$query_target_feature_id}{strand}=$strand;
$align{qt}{$query_target_feature_id}{indentity}=$indentity;
$align{qt}{$query_target_feature_id}{q_cov}=$q_cov;
$align{qt}{$query_target_feature_id}{t_cov}=$t_cov;
$align{target}{$target_feature_id}{target_scf}=$target_scf;
$align{target}{$target_feature_id}{target_start}=$target_start;
$align{target}{$target_feature_id}{target_end}=$target_end;
push(@pairs,$query_target_feature_id);
}
close BLAST;
}elsif($alignment_type eq "blat_psl"){ # https://genome.ucsc.edu/FAQ/FAQformat.html#format2
my $big=1;
my $detail=1;
if($k=~ /blat_block_show/){
my $error="error: blat_block_show in $k format error, should like \\t/blat_block_show->1:1 or blat_block_show->1:0 or blat_block_show->0:1\n";
if($k=~ /blat_block_show->([01]):[01]/){
$big=$1;
$detail=$2;
die "$error\n" if($big + $detail ==0);
}else{
die "$error\n";
}
}
if($alignment=~ /\.gz/){
if($sort){
open BLAT,"gzip -dc $alignment|awk '{if(\$1==\"psLayout\"){flag=1}if(flag==1){if(NR>=6)print \$0}else{print \$0}}'|sort -k 4nr,4nr -k 1,1 -k 2,2|" or die "$?";
}else{
open BLAT,"gzip -dc $alignment|awk '{if(\$1==\"psLayout\"){flag=1}if(flag==1){if(NR>=6)print \$0}else{print \$0}}'|" or die "$?";
}
print "$alignment is gz file\n";
}else{
if($sort){
open BLAT,"cat $alignment|awk '{if(\$1==\"psLayout\"){flag=1}if(flag==1){if(NR>=6)print \$0}else{print \$0}}'|sort -k 4nr,4nr -k 1,1 -k 2,2|" or die "$?";
}else{
open BLAT,"cat $alignment|awk '{if(\$1==\"psLayout\"){flag=1}if(flag==1){if(NR>=6)print \$0}else{print \$0}}'|" or die "$?";
}
print "$alignment is plain file\n";
}
while(<BLAT>){
chomp;
next if($_=~ /^#/ ||$_=~ /^\s*$/);
#print "line$. is $_\n";
my @arr=split(/\s+/,$_);
die "error:alignment sholud be 21 columns in $alignment\n" if(@arr!=21);
my $query_scf=$arr[9];
my $target_scf=$arr[13];
my $query_start=($arr[11] ==0)? 1:$arr[11];
my $query_end=$arr[12];
my $target_start=($arr[15] ==0)? 1:$arr[15];
my $target_end=$arr[16];
my $strand=$arr[8];
if($strand eq "+" || $strand eq "-"){
die "error:here1 in line$.:$_ \n" if($query_start > $query_end);
die "error:here2 in line$.:$_ \n" if($target_start > $target_end);
}else{
die "error: blat not support strand $strand in line$.:$_ yet\n";
}
if($arr[19]=~ /\d,\d/ && $detail){
my @blocksize=split(/,/, $arr[18]);
my @detail_q=split(/,/, $arr[19]);
my @detail_t=split(/,/, $arr[20]);
for my $i(0..scalar(@detail_q)-1){
my $q_start=$detail_q[$i];
$q_start = 1 if($q_start ==0);
my $q_end=$q_start+$blocksize[$i];
my $t_start=$detail_t[$i];
$t_start = 1 if($t_start ==0);
my $t_end=$t_start+$blocksize[$i];
die "error:blat max($q_start, $q_end) > $arr[10] || max($t_start, $t_end)>$arr[14]\n" if(max($q_start, $q_end) > $arr[10] || max($t_start, $t_end)>$arr[14]);
my $query_feature_id="$query_name.$query_scf.$q_start.$q_end.$k_index.$strand";
my $target_feature_id="$target_name.$target_scf.$t_start.$t_end.$k_index.$strand";
my $query_target_feature_id="$query_feature_id -> $target_feature_id";
my $indentity="null";
my $q_cov=(abs($q_end -$q_start)+1)/$arr[10] * 100;
my $t_cov=(abs($t_end-$t_start)+1)/$arr[14] * 100;
$align{query}{$query_feature_id}{query_scf}=$query_scf;
$align{query}{$query_feature_id}{query_start}=$q_start;
$align{query}{$query_feature_id}{query_end}=$q_end;
$align{qt}{$query_target_feature_id}{strand}=$strand;
$align{qt}{$query_target_feature_id}{indentity}=$indentity;
$align{qt}{$query_target_feature_id}{q_cov}=$q_cov;
$align{qt}{$query_target_feature_id}{t_cov}=$t_cov;
$align{target}{$target_feature_id}{target_scf}=$target_scf;
$align{target}{$target_feature_id}{target_start}=$t_start;
$align{target}{$target_feature_id}{target_end}=$t_end;
push(@pairs,$query_target_feature_id);
}
}
if($big){
die "\nerror:$query_scf of $query_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$query_name}{$query_scf});
die "\nerror:$target_scf of $target_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$target_name}{$target_scf});
my $query_feature_id="$query_name.$query_scf.$query_start.$query_end.$k_index.$strand";
my $target_feature_id="$target_name.$target_scf.$target_start.$target_end.$k_index.$strand";
my $query_target_feature_id="$query_feature_id -> $target_feature_id";
my $indentity=($arr[0]-$arr[1])/$arr[0];
my $q_cov=(abs($arr[12]-$arr[11])+1)/$arr[10] * 100;
my $t_cov=(abs($arr[16]-$arr[15])+1)/$arr[14] * 100;
$align{query}{$query_feature_id}{query_scf}=$query_scf;
$align{query}{$query_feature_id}{query_start}=$query_start;
$align{query}{$query_feature_id}{query_end}=$query_end;
$align{qt}{$query_target_feature_id}{strand}=$strand;
$align{qt}{$query_target_feature_id}{indentity}=$indentity;
$align{qt}{$query_target_feature_id}{q_cov}=$q_cov;
$align{qt}{$query_target_feature_id}{t_cov}=$t_cov;
$align{target}{$target_feature_id}{target_scf}=$target_scf;
$align{target}{$target_feature_id}{target_start}=$target_start;
$align{target}{$target_feature_id}{target_end}=$target_end;
push(@pairs,$query_target_feature_id);
}
}
close BLAT;
}elsif($alignment_type eq "mummer_coords"){ # https://mummer4.github.io/tutorial/tutorial.html /hwfssz4/BC_COM_P0/F18FTSECKF1389/ASPjisD/mummer/mummer-4.0.0beta2/
if($alignment=~ /\.coords$/){
if($sort){
open M,"cat $alignment|awk 'NR>=6'|sort -k 7nr,7nr -k 8nr,8nr -k 10nr,10nr -k 18,19|" or die "$?";
}else{
open M,"$alignment|awk 'NR>=6'|" or die "$?";
}
print "$alignment is plain file\n";
}elsif($alignment=~ /\.gz/){
if($sort){
open M,"gzip -dc $alignment|awk 'NR>=6'|sort -k 7nr,7nr -k 8nr,8nr -k 10nr,10nr -k 18,19|" or die "$?";
}else{
open M,"gzip -dc $alignment|awk 'NR>=6'|" or die "$?";
}
print "$alignment is gz file\n";
}else{
die "\nerror:$alignment should end with coords or gz\n";
}
while(<M>){
chomp;
next if($_=~ /^#/ ||$_=~ /^\s*$/);
#print "line$. is $_\n";
my @arr=split(/\s+/,$_);
die "error:alignment sholud be 20 columns in $alignment\n" if(@arr!=20);
my $query_scf=$arr[19];
my $target_scf=$arr[18];
my $query_start=($arr[4] >$arr[5])? $arr[5]:$arr[4];
my $query_end=($arr[4] >$arr[5])? $arr[4]:$arr[5];
my $target_start=$arr[1];
my $target_end=$arr[2];
die "die:error $arr[2]<$arr[1]\n" if($arr[2]<$arr[1]);
my $strand=($arr[4] >$arr[5])? "-":"+";
die "\nerror:$query_scf of $query_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$query_name}{$query_scf});
die "\nerror:$target_scf of $target_name in $alignment not in --list\n" if(not exists $conf->{sample_scf}{$target_name}{$target_scf});
my $query_feature_id="$query_name.$query_scf.$query_start.$query_end.$k_index.$strand";
my $target_feature_id="$target_name.$target_scf.$target_start.$target_end.$k_index.$strand";
my $query_target_feature_id="$query_feature_id -> $target_feature_id";
my $indentity=$arr[10];
my $q_cov=$arr[16];
my $t_cov=$arr[15];
$align{query}{$query_feature_id}{query_scf}=$query_scf;
$align{query}{$query_feature_id}{query_start}=$query_start;
$align{query}{$query_feature_id}{query_end}=$query_end;
$align{qt}{$query_target_feature_id}{strand}=$strand;
$align{qt}{$query_target_feature_id}{indentity}=$indentity;
$align{qt}{$query_target_feature_id}{q_cov}=$q_cov;
$align{qt}{$query_target_feature_id}{t_cov}=$t_cov;
$align{target}{$target_feature_id}{target_scf}=$target_scf;
$align{target}{$target_feature_id}{target_start}=$target_start;
$align{target}{$target_feature_id}{target_end}=$target_end;
push(@pairs,$query_target_feature_id);
}
close M;
}else{
die "error: not support alignment_type $alignment_type yet\n"
}
($synteny_gff_q, $synteny_setting_conf_q,$synteny_gff_t, $synteny_setting_conf_t, $cross_link_conf) = &synteny_common_write(\@pairs, \%align, $arr);
return ($synteny_gff_q, $synteny_setting_conf_q,$synteny_gff_t, $synteny_setting_conf_t, $cross_link_conf);
}
sub synteny_common_write(){
my ($pairs, $align, $arr)=@_;
my @pairs=@$pairs;
my %align=%$align;
my ($synteny_order,$query_name,$target_name,$alignment,$alignment_type,$crosslink_shape,$forward_color,$forward_opacity,$reverse_color,$reverse_opacity, $cross_link_shift_y)=@$arr;
my ($synteny_gff_q, $synteny_setting_conf_q,$synteny_gff_t, $synteny_setting_conf_t, $cross_link_conf);
my $cross_link_opacity;
my $cross_link_color;
my (%qid, %tid, %qtid);
for my $pair(@pairs){
my ($query_feature_id, $target_feature_id)=split(/\s+->\s+/, $pair);
my $query_start=$align{query}{$query_feature_id}{query_start};
my $query_end=$align{query}{$query_feature_id}{query_end};
my $query_scf=$align{query}{$query_feature_id}{query_scf};
my $target_start=$align{target}{$target_feature_id}{target_start};
my $target_end=$align{target}{$target_feature_id}{target_end};
my $target_scf=$align{target}{$target_feature_id}{target_scf};
my $strand=$align{qt}{$pair}{strand};
if(not exists $qid{$query_feature_id}){
$synteny_gff_q.="$query_scf\tadd\tsynteny\t$query_start\t$query_end\t.\t$strand\t.\tID=$query_feature_id;\n";
$synteny_setting_conf_q.="$query_feature_id\tfeature_shape\trect\n";
$synteny_setting_conf_q.="$query_feature_id\tfeature_height_ratio\t1\n";
$synteny_setting_conf_q.="$query_feature_id\tfeature_height_unit\tbackbone\n";
#$synteny_setting_conf_q.="$query_feature_id\tfeature_color\t$feature_color\n";
$synteny_setting_conf_q.="$query_feature_id\tfeature_opacity\t0\n";
$synteny_setting_conf_q.="$query_feature_id\tdisplay_feature_label\tno\n";
$synteny_setting_conf_q.="$query_feature_id\tfeature_order\t$synteny_order\n";
$qid{$query_feature_id}="";
}
if(not exists $tid{$target_feature_id}){
$synteny_gff_t.="$target_scf\tadd\tsynteny\t$target_start\t$target_end\t.\t$strand\t.\tID=$target_feature_id;\n";
$synteny_setting_conf_t.="$target_feature_id\tfeature_shape\trect\n";
$synteny_setting_conf_t.="$target_feature_id\tfeature_height_ratio\t1\n";
$synteny_setting_conf_t.="$target_feature_id\tfeature_height_unit\tbackbone\n";
#$synteny_setting_conf_t.="$target_feature_id\tfeature_color\t$feature_color\n";
$synteny_setting_conf_t.="$target_feature_id\tfeature_opacity\t0\n";
$synteny_setting_conf_t.="$target_feature_id\tdisplay_feature_label\tno\n";
$synteny_setting_conf_t.="$target_feature_id\tfeature_order\t$synteny_order\n";
$tid{$target_feature_id}="";
}
if($strand eq "+"){
$cross_link_color=$forward_color;
$cross_link_opacity=$forward_opacity;
}elsif($strand eq "-"){
$cross_link_color=$reverse_color;
$cross_link_opacity=$reverse_opacity;
}else{
die "\nerror:srand $strand\n";
}
$cross_link_opacity*=($align{qt}{$pair}{indentity}/100);
my $q_cov=$align{qt}{$pair}{q_cov};
my $t_cov=$align{qt}{$pair}{t_cov};
if(not exists $qtid{"$query_feature_id.$target_feature_id"}){
my $feature_popup_title="query -> $query_scf:$query_start:$query_end;target -> $target_scf:$target_start:$target_end;strand -> $strand;indentity -> $align{qt}{$pair}{indentity}%;coverage -> query:$q_cov%;target:$t_cov%";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcross_link_shape\t$crosslink_shape\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcross_link_anchor_pos\tlow_up\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcross_link_color\t$cross_link_color\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcross_link_opacity\t$cross_link_opacity\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcross_link_shift_y\t$cross_link_shift_y\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tcrosslink_stroke_style\tstroke:black;stroke-width:0.2;\n";
$cross_link_conf.="$query_feature_id\t$target_feature_id\tfeature_popup_title\t$feature_popup_title\n";
$qtid{"$query_feature_id.$target_feature_id"}="";
}
}
return $synteny_gff_q, $synteny_setting_conf_q,$synteny_gff_t, $synteny_setting_conf_t, $cross_link_conf;
}
sub reads_mapping(){
my ($gff, $conf)=@_;
my $ex="";
unless(exists $conf->{reads_mapping} && $conf->{reads_mapping}){
print "reads_mapping not\n";
return 0;
}
print "reads_mapping start\n";
my $k_index;
my (%outname);
my @env=("samtools");
&check_env_exist(@env);
my %show_types;
@{$show_types{short_reads}}=(qr/^rainbow:color->[^:]+:opacity->[\d\.]+:cross_link_width_ellipse->[\d\.]+/,"stack",qr/^paired:color->[^:]+:opacity->[\d\.]+:cross_link_height_line->[\d\.]+/);
@{$show_types{long_reads}}=("stack");
@{$show_types{vcf}}=("stack");
my @highs=("highlight_vlines", "start_end_xaxis","color_height_cs", "display_feature_label", "feature_x_extent","ylabel");
my @mapping_types=("short_reads", "long_reads", "vcf");
for my $k (@{$conf->{reads_mapping}}){
$k_index++;
&check_highs(\@highs,$k);
print "$k_index is $k\n\n";
my @ks = split(/\t+/, $k);
my @infos=split(/,/, $ks[0]);
my $infos_len=scalar(@infos);
if($infos_len != 17){
die "\nerror: reads_mapping should separate by \\t, and have 17 colums for reads_mapping=$k, but only have $infos_len\nvalid like reads_mapping=$ex\n";
}
my ($reads_type,$reads_order,$sample,$scf,$block_flag,$mapping_file,$show_type,$yaxis,$ytick_flag,$yaxis_show,$ytick_label,$hgrid_flag,$tick_color,$tick_opacity,$tick_border,$label_size,$mapqs) = @infos;
#ylabel->illuminate read depth,fontsize:10,color:black
die "\nerror: reads_order should be number, not $reads_order\n" if($reads_order!~ /^-?\d+$/);
#reads_mapping=long_reads,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,10->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3 highlight_hgrid->26:2:green,28:2:black start_end_xaxis->61:661,711:1311,1361:1961
my $refasta;
($mapping_file, $refasta)=&check_sort_bam($mapping_file, $reads_type);
die "\nerror: not support $reads_type~ only support @mapping_types\n" if(! grep(/^$reads_type$/, @mapping_types));
&show_type_check($show_type,\@{$show_types{$reads_type}});
die "\nerror: mapqs $mapqs should be number which >=0 , and like 0:10:40 which mean will show mapping read which mapq>=0, if mapq>=40 will use the same opacity\n" if($mapqs!~ /^\d+:\d+:\d+$/);
for(my $i=0;$i<$infos_len;$i++){
next if($i==8);
$infos[$i]=~ s/\s//g;
}
die "\nerror: block_flag should >=0, 0 mean all\n" if($block_flag<0 ||$block_flag!~ /^\d+$/);
die "\nerror: $sample or $scf not are friends in $k\n" if(not exists $gff->{$sample}->{scf}->{$scf});
die "\nerror: $sample don't have $block_flag fragments in $k\n" if($block_flag!=0 && not exists $gff->{$sample}->{chooselen_single}->{$block_flag});
for my $block_index(keys %{$gff->{$sample}->{chooselen_single}}){
print "block_index is $block_index,$sample\n";
next if($block_flag != 0 && $block_flag != $block_index);
my @scfs=keys %{$gff->{$sample}->{block2}->{$block_index}};
next if($scf ne $scfs[0]);
my @yaxis_list=split(/->/,$yaxis);
die "\nerror:yaxis_list neet two elements, not $yaxis, should like 10->50\n" if(@yaxis_list!=2 || $yaxis!~ /[-\d\.]+->[-\d\.]+/);
my @yaxis_show_list=split(/->/,$yaxis_show);
die "\nerror:yaxis_list neet three elements, not $yaxis_show, sholud like 10->30->5\n" if(@yaxis_show_list!=3 || $yaxis_show!~ /[-\d\.]+->[-\d\.]+->[-\d\.]+/);
#my $tick="$yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$ytick_label";
my @label_sizes=split(/:/,$label_size);
die "\nerror:label_size $label_size format like 6:6 for $k\n" if(@label_sizes!=2);
my ($mapping_label_size, $tick_label_size)=@label_sizes;
my $block_start_bp = $gff->{$sample}->{chooselen_single}->{$block_index}->{start};
my $block_end_bp = $gff->{$sample}->{chooselen_single}->{$block_index}->{end};
my ($ylabel_gff, $ylabel_setting_conf, $ylabel_cross_link_conf)=&plot_ylabel($k, $block_start_bp, $block_end_bp, $sample, $block_index, $scf, $k_index, $yaxis, $reads_type, \@yaxis_list);
my $prefix_ylabel="$sample.$scf.$block_index.$k_index.$reads_type.ylabel";
%outname = &gather_gff_conf_link($prefix_ylabel,$ylabel_gff,$ylabel_setting_conf,$ylabel_cross_link_conf, \%outname, $sample);
if($ytick_flag){
my ($ytick_gff, $ytick_setting_conf, $cross_link_conf)=&feature_ytick($yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$yaxis_show_list[2], $ytick_label,$sample, $scf, $block_index, $gff,$k_index, $hgrid_flag, $tick_color, $tick_opacity, $tick_border, $k, $tick_label_size, $reads_type);
my $prefix="$sample.$scf.$block_index.$k_index.ytick";
%outname = &gather_gff_conf_link($prefix,$ytick_gff,$ytick_setting_conf,$cross_link_conf, \%outname, $sample);
}
my %highss = &get_regions(\@highs, $k, $block_start_bp, $block_end_bp);
next if(not exists $highss{start_end_xaxis});
my @start_end_xaxis = @{$highss{start_end_xaxis}};
print "start_end_xaxis is @start_end_xaxis\n";
my $max_depth=&get_max_depth(\@start_end_xaxis,$mapping_file,$sample,$scf, $reads_type);
print "max_depth max_depth is $max_depth\n";
for my $rg(@start_end_xaxis){
my ($rg_start, $rg_end)=split(/,/, $rg);
print "rg is $rg, :$rg_start,$rg_end\n";
my ($mapping_gff, $mapping_setting_conf, $cross_link_conf)=&reads_mapping_run($yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$yaxis_show_list[2],$ytick_label,$mapping_file, $sample,$scf,$block_index, $gff, $k, $mapping_label_size, $k_index, $reads_type, $rg_start, $rg_end, $max_depth,$reads_order, $highss{color_height_cs}, $show_type, $mapqs,$refasta);
my $prefix="$sample.$scf.$block_index.$k_index.$rg_start.$rg_end.mapping";
%outname = &gather_gff_conf_link($prefix,$mapping_gff,$mapping_setting_conf,$cross_link_conf, \%outname, $sample);
}
}
}
&write_gff_conf_link(\%outname, "read_mapping");
}
sub show_type_check(){
my ($show_type,$show_types)=@_;
my @show_types=@$show_types;
my $show_type_flag=0;
for my $t(@show_types){
$show_type_flag++ if($show_type=~ /$t/);
}
die "\nerror: $show_type not supported, only support @show_types\n" if($show_type_flag!=1);
}
sub plot_ylabel(){
my ($k, $block_start_bp, $block_end_bp, $sample, $block_index, $scf, $k_index, $yaxis, $type, $yaxis_list)=@_;
my $ylabel_gff="";
my $ylabel_setting_conf="";
my $ylabel_cross_link_conf="";
my @yaxis_list=@$yaxis_list;
my $feature_shift_x;
my $feature_shift_y;
if($yaxis_list[0]=~ /^\+?\d/ && $yaxis_list[1]=~ /^\+?\d/){
$feature_shift_y=(abs($yaxis_list[0])+abs($yaxis_list[1]))/2;
$feature_shift_y="-$feature_shift_y";
}elsif($yaxis_list[0]=~ /^-\d/ && $yaxis_list[1]=~ /^-\d/){
$feature_shift_y=(abs($yaxis_list[0])+abs($yaxis_list[1]))/2;
$feature_shift_y="+$feature_shift_y";
}else{
die "\nerror:plot_ylabel @yaxis_list\n";
}
if($k=~ /\sylabel->([^,]+),gap:([\d\.]+)bp,fontsize:([\d\.]+),color:(\S+)/){
my $ylabel_content=$1;
my $gap=$2;
my $ylabel_fontsize=$3;
my $ylabel_color=$4;
my $ylabel_id="$sample.$scf.$block_index.$block_start_bp.$block_end_bp.$k_index.$type.ylabel";
$ylabel_id.=($yaxis=~ /^\d/)? "+":"-";
my $feature_shift_x=5+$gap;
$ylabel_gff.="$scf\tadd\tylabel\t$block_end_bp\t$block_end_bp\t.\t+\t.\tID=$ylabel_id;\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_label_color\t$ylabel_color\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_shift_x\t$feature_shift_x\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_height_ratio\t0\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_height_unit\tpercent\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_label_size\t$ylabel_fontsize\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_shift_y\t$feature_shift_y\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_shift_y_unit\tpercent\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_label\t$ylabel_content\n";
$ylabel_setting_conf.="$ylabel_id\tdisplay_feature_label\tyes\n";
$ylabel_setting_conf.="$ylabel_id\tpos_feature_label\tright_low\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_label_auto_angle_flag\t0\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_color\twhite\n";
$ylabel_setting_conf.="$ylabel_id\tfeature_shape\trect\n";
$ylabel_setting_conf.="$ylabel_id\tlabel_text_alignment_baseline\tmiddle\n";
}elsif($k=~ /\sylabel->/){
die "\nerror:k is $k\n";
}
return ($ylabel_gff, $ylabel_setting_conf, $ylabel_cross_link_conf);
}
sub check_highs(){
my ($highs,$k)=@_;
my @highs=@$highs;
for my $h(@highs){
die "\nerror: $h in $k should like $h->\n" if($k=~ /\s$h/ && $k!~ /\s$h->/);
die "\nerror: should use \\t,not just space key, for $h in $k \n" if($k=~ / $h->/);
}
return 0;
}
sub write_gff_conf_link(){
my ($outname, $prefix)=@_;
my %outname=%$outname;
for my $s(keys %outname){
if($outname{$s}{gff}){
`set -vex;cat @{$outname{$s}{gff}} >$s.$prefix.gff;echo output $s.$prefix.gff`;
}
if($outname{$s}{conf}){
`set -vex;cat @{$outname{$s}{conf}} > $s.$prefix.setting.conf;echo output $s.$prefix.setting.conf;echo rm @{$outname{$s}{gff}} @{$outname{$s}{conf}};`;
}
if(exists $outname{$s}{crosslink}){
`set -vex;cat @{$outname{$s}{crosslink}} >$s.$prefix.crosslink;echo output $s.$prefix.crosslink;echo;rm @{$outname{$s}{crosslink}}`;
}
}
print "$prefix end\n";
}
sub gather_gff_conf_link(){
my ($prefix,$gff,$setting_conf,$cross_link_conf, $outname, $sample)=@_;
my %outnames=%$outname;
if($gff){
my $out_gff="$prefix.gff";
print "\noutput $out_gff\n";
push @{$outnames{$sample}{gff}},$out_gff;
open GFF,">$out_gff" or die "$!";
print GFF "$gff";
close GFF;
}else{
print "\nno $prefix.gff for $sample\n";
}
if($setting_conf){
my $out_conf="$prefix.setting.conf";
push @{$outnames{$sample}{conf}},$out_conf;
print "\noutput $out_conf\n";
open CONF,">$out_conf" or die "$!";
print CONF "$setting_conf";
close CONF;
}else{
print "\nno $prefix.setting.conf for $sample\n";
}
if($cross_link_conf){
my $out_crosslink_conf="$prefix.crosslink.conf";
push @{$outnames{$sample}{crosslink}},$out_crosslink_conf;
print "\noutput $out_crosslink_conf\n";
open CONF,">$out_crosslink_conf" or die "$!";
print CONF "$cross_link_conf";
close CONF;
}else{
print "\nno $prefix.crosslink.conf for $sample\n";
}
return %outnames;
}
sub check_env_exist(){
my @envs=@_;
for my $env(@envs){
`which $env 2>/dev/null`;
die "\nerror: $env not exists by which $env, should add $env path to PATH\n" if($?);
}
}
sub check_sort_bam(){
my ($mapping_file, $reads_type)=@_;
die "\nerror: $mapping_file is a sorted bam file? if true, please rename it to *sort*.bam\n" if($mapping_file!~ /.*sort.*.bam/ && $reads_type ne "vcf");
die "\nerror:$mapping_file should like xx.mapping.bam:xx.ref.fa\n" if($mapping_file!~ /^(\S+):(\S+)$/);
my @arr=split(/:/,$mapping_file);
for my $f(@arr){
die "\nerror: file $f in $mapping_file not exists\n" if(! -f "$f");
}
return @arr;
}
sub get_max_depth(){
my ($start_end_xaxis, $mapping_file,$sample,$scf, $reads_type)=@_;
my @start_end_xaxis=@$start_end_xaxis;
my $max_depth=0;
return 1 if($reads_type eq "vcf");
for my $rg (@start_end_xaxis){
my ($rg_start, $rg_end)=split(/,/, $rg);
my $cmd="samtools depth -r $scf:$rg_start-$rg_end $mapping_file|awk '{print \$NF}'|sort -k 1nr|head -1";
print "cmd is $cmd\n";
my $rg_depth=`$cmd`;
die "\nerror:$cmd\n" if($?);
$max_depth=$rg_depth if($max_depth < $rg_depth);
}
return $max_depth;
}
sub hist_scatter_line(){
my ($gff, $conf)=@_;
my $ex="s2,s2000,0,100,path_map.sort.bam,10->50,ytick_flag,20->30,ytick_label_text,hgrid_flag,tick_color\n#sample,scf,block_flag,window_size,depth_file,yaxis,ytick_flag,yaxis_show,ytick_label,hgrid_flag,tick_color";
unless(exists $conf->{hist_scatter_line} && $conf->{hist_scatter_line}){
print "hist_scatter_line not\n";
return 0;
}
print "hist_scatter_line start\n";
my $k_index;
my (%outname);
my @highs=("highlight_columns", "highlight_hgrid", "start_end_xaxis", "ylabel");
for my $k (@{$conf->{hist_scatter_line}}){
$k_index++;
&check_highs(\@highs,$k);
print "$k_index is $k\n\n";
my @ks = split(/\t+/, $k);
my @infos=split(/,/, $ks[0]);
#highlight_hgrid->26:2:green,28:2:black highlight_columns->0:20:green:0.7,20:100:black:0.5 start_end_xaxis->61:661,711:1311,1361:1961
my $infos_len=scalar(@infos);
if($infos_len != 17){
die "\nerror: hist_scatter_line should have 17 colums for hist_scatter_line=$k, but only have $infos_len\nvalid like hist_scatter_line=$ex\n";
}
my ($depth_type,$depth_order,$sample,$scf,$block_flag,$window_size,$depth_file,$color_opacity,$yaxis,$ytick_flag,$yaxis_show,$ytick_label,$hgrid_flag,$tick_color,$tick_opacity,$tick_border,$label_size) = @infos;
die "\nerror:color_opacity $color_opacity should be like color->green:opacity->0.9\n" if($color_opacity!~ /^color->([^:]+):opacity->([\d\.+])$/);
my $the_color=$1;
my $the_opacity=$2;
die "\nerror: depth_order should be number, not $depth_order\n" if($depth_order!~ /^-?\d+$/);
my @depth_types=("hist", "scatter", "scatter_line");
die "\nerror: not support $depth_type~ only support @depth_types\n" if(! grep(/^$depth_type$/, @depth_types));
$depth_file=~ /^([^:]+):([^:]+)$/;
die "\nerror: $1 not exists in $depth_file for hist_scatter_line=$k\n" if(! -f $1);
die "\nerror: $2 not exists in $depth_file for hist_scatter_line=$k\n" if(! -f $2);
for(my $i=0;$i<$infos_len;$i++){
next if($i==8);
$infos[$i]=~ s/\s//g;
}
die "\nerror: block_flag should >=0, 0 mean all\n" if($block_flag<0 ||$block_flag!~ /^\d+$/);
die "\nerror: window_size should >=1\n" if($window_size!~ /^\d+$/);
die "\nerror: $sample or $scf not are friends in $k\n" if(not exists $gff->{$sample}->{scf}->{$scf});
die "\nerror: $sample don't have $block_flag fragments in $k\n" if($block_flag!=0 && not exists $gff->{$sample}->{chooselen_single}->{$block_flag});
for my $block_index(keys %{$gff->{$sample}->{chooselen_single}}){
print "block_index is $block_index,$sample\n";
next if($block_flag != 0 && $block_flag != $block_index);
my @scfs=keys %{$gff->{$sample}->{block2}->{$block_index}};
next if($scf ne $scfs[0]);
my @yaxis_list=split(/->/,$yaxis);
die "\nerror:yaxis_list neet two elements, not $yaxis, should like 10->50\n" if(@yaxis_list!=2 || $yaxis!~ /[-\d\.]+->[-\d\.]+/);
my @yaxis_show_list=split(/->/,$yaxis_show);
die "\nerror:yaxis_list neet three elements, not $yaxis_show, sholud like 10->30->5\n" if(@yaxis_show_list!=3 || $yaxis_show!~ /[-\d\.]+->[-\d\.]+->[-\d\.]+/);
#my $tick="$yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$ytick_label";
my @label_sizes=split(/:/,$label_size);
die "\nerror:label_size $label_size format like 6:6 for $k\n" if(@label_sizes!=2);
my ($depth_label_size, $tick_label_size)=@label_sizes;
my $block_start_bp = $gff->{$sample}->{chooselen_single}->{$block_index}->{start};
my $block_end_bp = $gff->{$sample}->{chooselen_single}->{$block_index}->{end};
my ($ylabel_gff, $ylabel_setting_conf, $ylabel_cross_link_conf)=&plot_ylabel($k, $block_start_bp, $block_end_bp, $sample, $block_index, $scf, $k_index, $yaxis, $depth_type, \@yaxis_list);
my $prefix_ylabel="$sample.$scf.$block_index.$k_index.$depth_type.ylabel";
%outname = &gather_gff_conf_link($prefix_ylabel,$ylabel_gff,$ylabel_setting_conf,$ylabel_cross_link_conf, \%outname, $sample);
if($ytick_flag){
my ($ytick_gff, $ytick_setting_conf, $cross_link_conf)=&feature_ytick($yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$yaxis_show_list[2], $ytick_label,$sample, $scf, $block_index, $gff,$k_index, $hgrid_flag, $tick_color, $tick_opacity, $tick_border, $k, $tick_label_size, $depth_type);
my $prefix="$sample.$scf.$block_index.$k_index.ytick";
%outname = &gather_gff_conf_link($prefix,$ytick_gff,$ytick_setting_conf,$cross_link_conf, \%outname, $sample);
}
my %highss = &get_regions(\@highs,$k, $block_start_bp, $block_end_bp);
next if(not exists $highss{start_end_xaxis});
my @start_end_xaxis = @{$highss{start_end_xaxis}};
#my @highlight_columns = @{$highss{highlight_columns}};
for my $rg(@start_end_xaxis){
my ($rg_start, $rg_end)=split(/,/, $rg);
print "rg is $rg :$rg_start,$rg_end\n";
my ($depth_gff, $depth_setting_conf, $cross_link_conf)=&hist_scatter_line_run($yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$yaxis_show_list[2],$ytick_label,$window_size, $depth_file, $sample,$scf,$block_index, $gff, $k, $depth_label_size, $k_index, $depth_type, $rg_start, $rg_end, $depth_order, $the_color, $the_opacity);
my $prefix="$sample.$scf.$block_index.$k_index.$rg_start.$rg_end.depth";
%outname = &gather_gff_conf_link($prefix,$depth_gff,$depth_setting_conf,$cross_link_conf, \%outname, $sample);
}
}
}
&write_gff_conf_link(\%outname, "hist_scatter_line");
}
sub reads_mapping_run(){
#&reads_mapping_run($yaxis_list[0],$yaxis_list[1],$yaxis_show_list[0],$yaxis_show_list[1],$yaxis_show_list[2],$ytick_label,$mapping_file, $sample,$scf,$block_index, $gff, $k, $mapping_label_size, $k_index, $reads_type, $rg_start, $rg_end, $max_depth);
my ($s1, $e1, $s2, $e2, $axis_gap,$title, $bam_file, $sample,$scf,$block, $gff, $info, $depth_label_size, $k_index, $read_type, $rg_start, $rg_end, $max_depth,$reads_order, $color_height_cs, $show_type,$mapqs, $refasta)=@_;
my $one_read_height=1;
my ($reads_gff, $reads_setting_conf, $cross_link_conf);
$color_height_cs="M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect" if(!$color_height_cs); #yellow
my %colors_height = &cigar_setting($color_height_cs);
if($read_type eq "vcf"){
($reads_gff, $reads_setting_conf, $cross_link_conf) = &check_vcf(\%colors_height, $bam_file, $sample, $scf, $rg_start, $rg_end, $k_index, $read_type, $s1, $e1, $info);
return ($reads_gff, $reads_setting_conf, $cross_link_conf);
}
my %reads=&get_mapping_reads($scf, $bam_file, $rg_start, $rg_end, $read_type,$reads_order, \%colors_height, $show_type, $mapqs, $refasta);
#my $read_num=scalar(keys %reads);
#die "read_num is $read_num\n";
my %reads_depth = &get_reads_depth(\%reads, $s1, $e1, $rg_start,$read_type, $show_type);
my %cross_link_pairs;
my $new_depth=0;
#my $one_read_height=(abs($s1-$e1))/$max_depth;
$max_depth=$reads_depth{max_depth}+0.5;
$one_read_height=(0.99 * abs($s1-$e1))/$max_depth;
print "max_depth is $max_depth, read_type is $read_type\n";
my $read_num;
my $read_shift_y;
my $read_shift_y_depth=0;
my $updown;
if($s1=~ /^\+?(\d+)/){
$updown=-1;
}elsif($s1=~ /^-(\d+)/){
$updown=1;
}else{
die "\nerror:11\n";
}
my $feature_height=1;
my $feature_opacity=1;
my $feature_color="black";
my $feature_shape="rect";
my $read_type_raw=$read_type;
$read_type="long_reads" if($show_type eq "stack");
my $read_number=scalar(keys %reads);
print "read number is $read_number\n";
for my $read_id(sort {$reads{$a}{ref_start}<=>$reads{$b}{ref_start}} keys %reads){
#print "read_id is $read_id\n";
$read_num++;
#my $read_id="$sample.$scf.$block.$rg_start.$rg_end.$k_index.$read_type.$read_num";
if($show_type =~ /^rainbow/){
#die "\nerror:rainbow\n";
#next if($reads{$read_id}{mate_read_id} eq "null"|| $reads{$read_id}{mate_ref} ne $reads{$read_id}{ref_id});
next if($reads{$read_id}{mate_read_id} eq "null");
#die "\nerror1:rainbow\n";
next if($reads{$read_id}{mate_ref} ne $reads{$read_id}{ref_id});
#die "\nerror2:rainbow\n";
my $mate=$reads{$read_id}{mate_read_id};
next if($reads{$mate}{cigar}{-1}{type} eq "fake"||$reads{$read_id}{cigar}{-1}{type} eq "fake");
#next if(($reads{$read_id}{cigar}{-1}{end}-$reads{$read_id}{cigar}{-1}{start})<147||($reads{$mate}{cigar}{-1}{end}-$reads{$mate}{cigar}{-1}{start})<147);
#next if($read_id!~ /90847/ && $read_id!~ /40151/);
}
if($read_type eq "short_reads" || $read_type eq "long_reads"){
#die "here\n" if($read_type eq "short_reads");
my ($r1_start,$r1_end,$r2_start,$r2_end);
# mate_read_id
my ($cr_id, $map_pos_start_cr, $map_pos_end_cr, $cr_type,$cr_order);
my $map_pos_strand_cr=$reads{$read_id}{strand};
my $read_shift_y_depth = $reads_depth{depth}{$read_id};
$read_shift_y_depth=0 if($show_type =~ /^rainbow/);
my $opacity_ratio_mapq=$reads{$read_id}{cigar}{-1}{mapq_percent};
for my $cr(sort {$a<=>$b} keys %{$reads{$read_id}{cigar}}){
$cr_type=$reads{$read_id}{cigar}{$cr}{type};
my $cg=$reads{$read_id}{cigar}{$cr}{cr};
($feature_color, $feature_height,$feature_opacity, $feature_shape)=&cs_color_height($cg, \%colors_height, $map_pos_strand_cr,$cr, $reads{$read_id}{r1_r2});
$feature_opacity*=$opacity_ratio_mapq;
$feature_opacity=0 if($cr_type eq "fake");
$feature_height *= $one_read_height;
$map_pos_start_cr=$reads{$read_id}{cigar}{$cr}{start};
$map_pos_end_cr=$reads{$read_id}{cigar}{$cr}{end};
$cr_order=$reads{$read_id}{cigar}{$cr}{order};
my $feature_popup_title="strand -> $map_pos_strand_cr;mapq -> $reads{$read_id}{cigar}{-1}{mapq};flag -> $reads{$read_id}{cigar}{-1}{flag};pos -> $reads{$read_id}{cigar}{-1}{pos};cigar ->$reads{$read_id}{cigar}{-1}{cigar}";
$read_shift_y = abs($s1) + $one_read_height * $read_shift_y_depth + ($one_read_height - $feature_height)/2;
$read_shift_y = ($updown == 1)? "+$read_shift_y":"-$read_shift_y";
$cr_id="$read_id.cr.$cr.$cg.$updown.$k_index";
#my $feature_shape="rect";
if($cr_type=~ /reverse/ || $cr_type=~ /forward/){
#$feature_shape="arrow";
my $feature_arrow_sharp_extent=($read_type eq "short_reads")? 0.08:0.01;
$reads_setting_conf.="$cr_id\tfeature_arrow_sharp_extent\t0\n";
$reads_setting_conf.="$cr_id\tfeature_arrow_width_extent\t$feature_arrow_sharp_extent\n";
$reads_setting_conf.="$cr_id\tfeature_popup_title\t$feature_popup_title\n";
}
if($cg=~ /^(\d+)I$/){
my $insert_height_tail_portion=0.1;
my $insert_feature_height=$insert_height_tail_portion * $feature_height;
my $insert_shift_y;
for my $tail(0..1){
my $insert_cr_id="$cr_id.$tail";
my $insert_map_pos_start_cr=$map_pos_start_cr- ($1-($map_pos_end_cr-$map_pos_start_cr))/10/2;
my $insert_map_pos_end_cr=$map_pos_end_cr + ($1-($map_pos_end_cr-$map_pos_start_cr))/10/2;
$insert_shift_y=($tail)? $read_shift_y+ $updown * (1-$insert_height_tail_portion)*$feature_height:$read_shift_y;
$reads_gff.="$scf\tadd\t$read_type_raw\t$insert_map_pos_start_cr\t$insert_map_pos_end_cr\t.\t$map_pos_strand_cr\t.\tID=$insert_cr_id;\n";
$reads_setting_conf.="$insert_cr_id\tfeature_shape\t$feature_shape\n";
$reads_setting_conf.="$insert_cr_id\tfeature_height_ratio\t$insert_feature_height\n";
$reads_setting_conf.="$insert_cr_id\tfeature_height_unit\tpercent\n";
$reads_setting_conf.="$insert_cr_id\tfeature_color\t$feature_color\n";
$reads_setting_conf.="$insert_cr_id\tfeature_shift_y\t$insert_shift_y\n";
$reads_setting_conf.="$insert_cr_id\tfeature_shift_y_unit\tpercent\n";
$reads_setting_conf.="$insert_cr_id\tfeature_order\t$cr_order\n";
$reads_setting_conf.="$insert_cr_id\tfeature_opacity\t$feature_opacity\n";
}
}
die "\nerror: cr_id is $cr_id\n" if($map_pos_start_cr eq "start");
$reads_gff.="$scf\tadd\t$read_type_raw\t$map_pos_start_cr\t$map_pos_end_cr\t.\t$map_pos_strand_cr\t.\tID=$cr_id;\n";
#if($cr_type ne "fake"){
# $reads_setting_conf.="$cr_id\tfeature_x_extent\t-0.5bp,+0.5bp\n";
#}
$feature_popup_title="mutation -> $cg,$map_pos_start_cr:$map_pos_end_cr";
$reads_setting_conf.="$cr_id\tfeature_shape\t$feature_shape\n";
$reads_setting_conf.="$cr_id\tfeature_height_ratio\t$feature_height\n";
$reads_setting_conf.="$cr_id\tfeature_height_unit\tpercent\n";
$reads_setting_conf.="$cr_id\tfeature_color\t$feature_color\n";
$reads_setting_conf.="$cr_id\tfeature_shift_y\t$read_shift_y\n";
$reads_setting_conf.="$cr_id\tfeature_shift_y_unit\tpercent\n";
$reads_setting_conf.="$cr_id\tfeature_order\t$cr_order\n";
$reads_setting_conf.="$cr_id\tfeature_opacity\t$feature_opacity\n";
$reads_setting_conf.="$cr_id\tfeature_popup_title\t$feature_popup_title\n" if($cr_type!~ /reverse/ && $cr_type!~ /forward/);
if($read_type eq "short_reads" && $cr == -1 && $reads{$read_id}{mate_read_id} ne "null" && ($reads{$read_id}{mate_ref} eq "=" || $reads{$read_id}{ref_id} eq $reads{$read_id}{mate_ref}) ){
next if(exists $reads{$read_id}{flag} && ($reads{$read_id}{flag} & 8));
my $mate_id=$reads{$read_id}{mate_read_id};
#die "ssread_id is $read_id, flag is $reads{$read_id}{flag}\n" if(!$mate_id);
my $mate_cg=$reads{$mate_id}{cigar}{$cr}{cr};
my $mate_cr_id="$mate_id.cr.$cr.$mate_cg.$updown.$k_index";
my $cross_link_order=$reads{$read_id}{cigar}{-1}{order};
next if(exists $cross_link_pairs{"$mate_id,$read_id"} || $reads{$read_id}{cigar}{$cr}{end} > $reads{$mate_id}{cigar}{$cr}{end});
my $cross_link_height_line=0.3;
my $cross_link_anchor_pos="medium_medium";
my $cross_link_shape="line";
my $cross_link_orientation_line="end,start";
my $cross_link_width_ellipse;
$feature_popup_title="$reads{$read_id}{ref_id} -> $reads{$read_id}{cigar}{-1}{start}:$reads{$read_id}{cigar}{-1}{end}:$reads{$read_id}{cigar}{-1}{cigar} : $reads{$mate_id}{cigar}{-1}{start}:$reads{$mate_id}{cigar}{-1}{end}:$reads{$mate_id}{cigar}{-1}{cigar}";
if($show_type=~ /^rainbow:color->([^:]+):opacity->([\d\.]+):cross_link_width_ellipse->([\d\.]+)/){
#rainbow:green:opacity1:cross_link_width_ellipse:0.01
my $cross_link_color=$1;
my $cross_link_opacity=$2*$opacity_ratio_mapq;
$cross_link_width_ellipse=$3;
my $out_r=abs($e1) - $one_read_height- abs($s1);
my $inner_r=abs($e1) - $one_read_height - abs($e1-$s1)*0.02-abs($s1);
my $cross_link_height_ellipse="$out_r,$inner_r";
$cross_link_anchor_pos=($updown == -1)? "up_up":"low_low";
$cross_link_shape="ellipse";
my $cross_link_orientation_ellipse=($updown == -1)? "up":"down";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_orientation_ellipse\t$cross_link_orientation_ellipse\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_height_ellipse\t$cross_link_height_ellipse\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_width_ellipse\t$cross_link_width_ellipse\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_color\t$cross_link_color\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_opacity\t$cross_link_opacity\n";
}elsif($show_type=~ /^paired:color->([^:]+):opacity->([\d\.]+):cross_link_height_line->([\d\.]+)/){
my $cross_link_opacity=$2*$opacity_ratio_mapq;
#die "$cross_link_opacity, $opacity_ratio_mapq, crid is $cr_id\n\n" if($cr_id=~ /1:7770:55632.14.66901400.66903400.read1.mate.cr.-1.0fake.-1.2/);
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_color\t$1\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_opacity\t$cross_link_opacity\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_height_line\t$3\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_orientation_line\t$cross_link_orientation_line\n";
}
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_anchor_pos\t$cross_link_anchor_pos\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_shape\t$cross_link_shape\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tcross_link_order\t$cross_link_order\n";
$cross_link_conf.="$cr_id\t$mate_cr_id\tfeature_popup_title\t$feature_popup_title\n";
$cross_link_pairs{"$read_id,$mate_id"}="" if(not exists $cross_link_pairs{"$read_id,$mate_id"});
}
}
}else{
die "die:\n";
}
}
die "\n\nerror:$info is no feature to plot\n\n" if(!$reads_gff);
return ($reads_gff, $reads_setting_conf, $cross_link_conf);
}
sub check_vcf(){
my ($colors_height, $vcf_file, $sample, $scf, $rg_start, $rg_end, $k_index, $read_type, $s1, $e1, $info)=@_;
my %colors_height=%$colors_height;
my $reads_gff="";
my $reads_setting_conf="";
my $cross_link_conf="";
my $feature_shift_y;
if($s1=~ /^\+?(\d+)/){
$feature_shift_y="-$1";
}elsif($s1=~ /^-(\d+)/){
$feature_shift_y="+$1";
}else{
die "\nerror:check_vcf s1 $s1 format \nerror\n";
}
my $display_feature_label="yes";
$display_feature_label="no" if($info=~ /\sdisplay_feature_label->no/);
die "\n\nerror: feature_x_extent should like feature_x_extent->-1bp,+1bp in $info\n" if($info=~ /\sfeature_x_extent/ && $info!~ /\sfeature_x_extent->[\d\.\+-]+bp,[\d\.\+-]+bp/);
if($vcf_file=~ /\.gz$/){
open VCF,"gzip -dc $vcf_file|" or die "open $vcf_file \nerror $?\n";
}else{
open VCF,"$vcf_file" or die "open $vcf_file \nerror $?\n";
}
while(<VCF>){
chomp;
next if($_=~ /^#/||$_=~ /^\s*$/);
##CHROM POS ID REF ALT QUAL FILTER
my @arr=split(/\t/,$_);
die "\nerror:vcf format \nerror in line$.:$_ in $vcf_file\n" if(@arr < 9);
my ($chr,$pos,$snpid,$ref_base,$query_base,$qual,$filter,$info,$format)=@arr[0..8];
next if($chr ne $scf || $pos < $rg_start || $pos > $rg_end || $ref_base eq $query_base);
#print "line is $_\n";
my $vcf_id="$sample.$scf.vcf.$pos.$ref_base.to.$query_base.$snpid.$k_index";
my $feature_label="$pos:$ref_base.to.$query_base";
my ($mutation_type, $mutation_length, $start, $end)=&check_vcf_mutation_type($ref_base, $query_base, $pos);
my $feature_color=$colors_height{$mutation_type}{color};
my $feature_height=$colors_height{$mutation_type}{height}*abs($s1-$e1);
my $feature_opacity=$colors_height{$mutation_type}{opacity};
if($mutation_length < $colors_height{$mutation_type}{limit_len}){
print "\nwarning:skip $_ in $vcf_file, because mutation_length is $mutation_length bp < $colors_height{$mutation_type}{limit_len} bp which is set in color_height_cs\n\n";
next;