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13-Graph_By_Finding_Best_MaxExtending_Random_Path_BioNano.pl
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13-Graph_By_Finding_Best_MaxExtending_Random_Path_BioNano.pl
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#!/usr/bin/perl
use strict;
no warnings;
=pod
use Graph;
use Graph::Directed;
use Graph::Undirected;
use Graph::Easy;
use Bio::SeqIO;
use Bio::Perl;
use Data::Dumper;
=cut
my $DEBUG=0;
my $inputfile=shift; #blasr_result output
#my $ContigNameListFile=shift; #all contig name contig_name.list
#my $MergedContigFile = shift; #output graph png
#my $out_cluster_file= shift; #output ctg clusters
my @ColumnNameArray = qw ( RefPos RefStrand Identity Score RefName QryName QryPos QryStart QryEnd QryLength RefStart RefEnd RefLength );
#my $Pair_Graph = Graph::Undirected->new;
my %Contig_Head_Tail_Query = % {( &ReadingStartPoint)[0]} ;
my %Contig_Gap_Length=%{(&ReadingGapInfo)[0]};
my %Reads_Pairs=();
#my ( $Finding_Best_Graph , $Output_Graph) = &initializeGraph( $ContigNameListFile );
#my %NodeHash = %{ ( &GenerateRecordHash( $inputfile ) )[0] };
#my %EdgeHash = %{ ( &GenerateRecordHash( $inputfile ))[1] };
#my %NodePairsHash = %{ ( &GenerateNodePairHash( $inputfile ))[0] };
#&drawEasyGraph ( $EasyGraph , $MergedContigFile , '01' );
############ 整合所有节点和边的信息，合并边，并且选择最好的pacbio作为其连接，并且计算两个NODE连接边的权重 #######
my ($ctg_ctg_count_point, $ctg_ctg_overlap_len_point, $ctg_ctg_ori_point, $ctg_ctg_chain_point,$ctg_ctg_line_point,$ctg_ctg_extend_point,$ctg_ctg_info_point)=&GenerateNodePairHash($inputfile);
my %ctg_ctg_count=%$ctg_ctg_count_point;
my %ctg_ctg_overlap_len=%$ctg_ctg_overlap_len_point;
my %ctg_ctg_ori=%$ctg_ctg_ori_point;
my %ctg_ctg_chain=%$ctg_ctg_chain_point;
my %ctg_ctg_line=%$ctg_ctg_line_point;
my %ctg_ctg_extend=%$ctg_ctg_extend_point;
my %ctg_ctg_info=%$ctg_ctg_info_point;
=pod
############ 过滤图中的边，如果一个节点的度>=3，则选择不同方向的两条边 ##########################################
%ctg_ctg_count = %{ (&Filtering_Edge (\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line))[0])};
%ctg_ctg_overlap_len=%{ (&Filtering_Edge (\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line))[1])};
%ctg_ctg_ori = %{ (&Filtering_Edge (\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line))[2])};
%ctg_ctg_chain = %{ (&Filtering_Edge (\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line))[3])};
%ctg_ctg_line = %{ (&Filtering_Edge (\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line))[4])};
########### 结束 ################################################################################################
=cut
############ 根据节点和边，将每对contig分别进行延伸，每次选择最好的边 ##########################################
&Finding_Best_Pathway(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line,\%Contig_Head_Tail_Query);
&Finding_MaxExtending_Pathway(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line,\%Contig_Head_Tail_Query, \%ctg_ctg_extend, \%ctg_ctg_info);
&Finding_Randoming_Pathway(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line,\%Contig_Head_Tail_Query, \%ctg_ctg_extend, \%ctg_ctg_info);
############ 根据Scaffold中Contig开头和末尾的Query分别进行延伸 ##################################################
############ End ################################################################################################
if($DEBUG==1){
# print Dumper(%NodePairsHash);
print Dumper(%ctg_ctg_count);
print Dumper(%ctg_ctg_overlap_len);
print Dumper(%ctg_ctg_ori);
print Dumper(%ctg_ctg_chain);
print Dumper(%ctg_ctg_line);
}
############## 读取Contig之间Gap的长度和信息 #####################################################################
sub ReadingGapInfo{
my %Contig_Gap=();
open GAP,"<Scaffold2Ctg_Gap.txt" or die $!;
#Super-Scaffold_5.5 Super-Scaffold_5.6 499 3029936 3030434
while(<GAP>){
chomp;
my $line=$_;
my @content=split /\s+/,$line;
$Contig_Gap{$content[0]}{$content[1]}=$content[2];
}
close(GAP);
return(\%Contig_Gap);
}
############# Contig之间Gap的长度和信息 ######################################################################
############## 读取Contig末端的Query，作为Graph 遍历的起点，以及用于判断两个节点间是否存在通路 ####################
sub ReadingStartPoint{
my %Scaffold_Contig_SEPoint=();
open Point,"<Contig_Head_Tail_Pacbio_Pos.txt" or die $!;
#R498_3390190_1/90_20012/0_19922 1 19922 19922 Super-Scaffold_14.29 9130 29199 963453 0 99.13
while(<Point>){
chomp;
my $line=$_;
my @content=split /\s+/,$line;
$content[0]=~/(\S+)\/0_\d+$/;
my $pacbio=$1;
$content[4]=~/(\S+)\.(\d+)$/;
my $scaffold=$1;
my $scaffold_sign=$2;
if($content[7]-$content[6]>=$content[5]){
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{0}=$content[8]; #Chain
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{1}=$content[5]; #Ref_start
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{2}=$content[6]; #Ref_end
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{3}=$content[7]; #Ref_len
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{4}=$content[1]; #Qry_start
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{5}=$content[2]; #Qry_end
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Head'}{$pacbio}{6}=$content[3]; #Qry_len
}
else{
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{0}=$content[8];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{1}=$content[5];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{2}=$content[6];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{3}=$content[7];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{4}=$content[1];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{5}=$content[2];
$Scaffold_Contig_SEPoint{$scaffold}{$scaffold_sign}{'Tail'}{$pacbio}{6}=$content[3];
}
}
close(Point);
return(\%Scaffold_Contig_SEPoint);
}
############## 统计支持ctg对的pacbio数，以及选择overlap最长的pacbio作为其连接两个ctg的信息 ########################
sub count_ctg_pair{
my $CtgPairsHash = shift;
my %NodePair=%{ $CtgPairsHash };
my %ctg_ctg_count=();
my %ctg_ctg_overlap_len=();
my %ctg_ctg_ori=();
my %ctg_ctg_chain=();
my %ctg_ctg_line=();
open PAIR,">ctg_pairs.txt" or die $!;
open ORI,">ctg_ctg_ori.txt" or die $!;
foreach my $key1 (keys %NodePair){
my %CtgPairPacbio= %{ $NodePair{$key1} };
my @content=split "-",$key1;
my $left_ctg=$content[0];
my $right_ctg=$content[1];
my $best_pacbio="";
foreach my $pacbio (keys %CtgPairPacbio){
$ctg_ctg_count{$left_ctg}{$right_ctg}++;
my $overlap_len=$CtgPairPacbio{$pacbio}{'First'}{'Score'};
if(!exists $ctg_ctg_overlap_len{$left_ctg}{$right_ctg}){
$ctg_ctg_overlap_len{$left_ctg}{$right_ctg}=0;
}
if($ctg_ctg_overlap_len{$left_ctg}{$right_ctg}<$overlap_len){
$ctg_ctg_overlap_len{$left_ctg}{$right_ctg}=$overlap_len;
$ctg_ctg_ori{$left_ctg}{$right_ctg}{1}=$CtgPairPacbio{$pacbio}{'First'}{'RefPos'};
$ctg_ctg_ori{$left_ctg}{$right_ctg}{2}=$CtgPairPacbio{$pacbio}{'Next'}{'RefPos'};
$ctg_ctg_ori{$right_ctg}{$left_ctg}{1}=$CtgPairPacbio{$pacbio}{'Next'}{'RefPos'};
$ctg_ctg_ori{$right_ctg}{$left_ctg}{2}=$CtgPairPacbio{$pacbio}{'First'}{'RefPos'};
$ctg_ctg_chain{$left_ctg}{$right_ctg}{1}=$CtgPairPacbio{$pacbio}{'First'}{'RefStrand'};
$ctg_ctg_chain{$left_ctg}{$right_ctg}{2}=$CtgPairPacbio{$pacbio}{'Next'}{'RefStrand'};
$ctg_ctg_chain{$right_ctg}{$left_ctg}{1}=$CtgPairPacbio{$pacbio}{'Next'}{'RefStrand'};
$ctg_ctg_chain{$right_ctg}{$left_ctg}{2}=$CtgPairPacbio{$pacbio}{'First'}{'RefStrand'};
$ctg_ctg_line{$left_ctg}{$right_ctg}=$left_ctg."-".$right_ctg."-".$pacbio;
$ctg_ctg_line{$right_ctg}{$left_ctg}=$right_ctg."-".$left_ctg."-".$pacbio;
$best_pacbio=$pacbio;
}
}
my $First_start=0;
my $First_end=0;
my $Next_start=0;
my $Next_end=0;
print ORI "$left_ctg\t$CtgPairPacbio{$best_pacbio}{'First'}{'RefLength'}\t$ctg_ctg_chain{$left_ctg}{$right_ctg}{1}\t$ctg_ctg_ori{$left_ctg}{$right_ctg}{1}\t$right_ctg\t$CtgPairPacbio{$best_pacbio}{'Next'}{'RefLength'}\t$ctg_ctg_chain{$left_ctg}{$right_ctg}{2}\t$ctg_ctg_ori{$left_ctg}{$right_ctg}{2}\t$ctg_ctg_count{$left_ctg}{$right_ctg}\n";
if($CtgPairPacbio{$best_pacbio}{'First'}{'RefStrand'}==0){
$First_start=$CtgPairPacbio{$best_pacbio}{'First'}{'RefStart'};
$First_end=$CtgPairPacbio{$best_pacbio}{'First'}{'RefEnd'};
}
elsif($CtgPairPacbio{$best_pacbio}{'First'}{'RefStrand'}==1){
$First_start=$CtgPairPacbio{$best_pacbio}{'First'}{'RefLength'}-$CtgPairPacbio{$best_pacbio}{'First'}{'RefEnd'};
$First_end=$CtgPairPacbio{$best_pacbio}{'First'}{'RefLength'}-$CtgPairPacbio{$best_pacbio}{'First'}{'RefStart'};
}
if($CtgPairPacbio{$best_pacbio}{'Next'}{'RefStrand'}==0){
$Next_start=$CtgPairPacbio{$best_pacbio}{'Next'}{'RefStart'};
$Next_end=$CtgPairPacbio{$best_pacbio}{'Next'}{'RefEnd'};
}
elsif($CtgPairPacbio{$best_pacbio}{'Next'}{'RefStrand'}==1){
$Next_start=$CtgPairPacbio{$best_pacbio}{'Next'}{'RefLength'}-$CtgPairPacbio{$best_pacbio}{'Next'}{'RefEnd'};
$Next_end=$CtgPairPacbio{$best_pacbio}{'Next'}{'RefLength'}-$CtgPairPacbio{$best_pacbio}{'Next'}{'RefStart'};
}
print PAIR "$left_ctg\t$CtgPairPacbio{$best_pacbio}{'First'}{'RefLength'}\t$right_ctg\t$CtgPairPacbio{$best_pacbio}{'Next'}{'RefLength'}\t$ctg_ctg_count{$left_ctg}{$right_ctg}\t$best_pacbio-$ctg_ctg_chain{$left_ctg}{$right_ctg}{1}-$CtgPairPacbio{$best_pacbio}{'First'}{'RefStart'}-$CtgPairPacbio{$best_pacbio}{'First'}{'RefEnd'}-$ctg_ctg_chain{$left_ctg}{$right_ctg}{2}-$CtgPairPacbio{$best_pacbio}{'Next'}{'RefStart'}-$CtgPairPacbio{$best_pacbio}{'Next'}{'RefEnd'}\t$best_pacbio-$CtgPairPacbio{$best_pacbio}{'First'}{'QryLength'}-$CtgPairPacbio{$best_pacbio}{'First'}{'QryStart'}-$CtgPairPacbio{$best_pacbio}{'First'}{'QryEnd'}-$CtgPairPacbio{$best_pacbio}{'Next'}{'QryStart'}-$CtgPairPacbio{$best_pacbio}{'Next'}{'QryEnd'}\n";
}
return(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line);
close(ORI);
close(PAIR);
}
sub initializeGraph{
my $ContigNameListFile = shift;
my $ContigGraph = Graph::Undirected->new;
my $EasyGraph = Graph::Easy->new( undirected => 1 );
open(IN, $ContigNameListFile ) or die("Cannot open $ContigNameListFile\n");
while ( my $line = <IN> ) {
chomp $line;
# contig0001_size5554
my $Contig = $line;
# $ContigGraph -> add_vertex( $Contig );
# $EasyGraph -> add_node( $Contig );
}
return $ContigGraph, $EasyGraph ;
}
sub drawEasyGraph{
my $EasyGraph = shift;
my $MergedContigFile = shift;
my $SubNum = shift;
my $graphviz = $EasyGraph -> as_graphviz();
# my $BACName = ( $MergedContigFile =~ m/TUG.(\S+).pacmerge(\d+)./ )[0];
# my $PacmergeNum = ( $MergedContigFile =~ m/TUG.(\S+).pacmerge(\d+)./ )[1];
# open my $DOT, "|dot -Tpng -o $MergedContigFile.png" or die ("Cannot open pipe to dot: $!");
# print $DOT $graphviz;
# close $DOT;
}
sub GenerateRecordHash{
my $inputfile = shift;
my %NodeHash = ();
my %EdgeHash = ();
my %NodePairsHash = ();
open(IN, $inputfile ) or die("Cannot open $inputfile\n");
while ( my $line = <IN> ) {
chomp $line;
my @Columns = split( /\s+/, $line );
my $RefName = $Columns[4];
my $QryName = $Columns[5];
my $Score = $Columns[3];
if ( ! exists ( $NodeHash{$RefName}{$QryName} ) ) {
for ( my $Idx = 0 ; $Idx < scalar( @Columns ) ; $Idx ++ ) {
my $ColumnName = $ColumnNameArray[$Idx];
$NodeHash{$RefName}{$QryName}{$ColumnName} = $Columns[$Idx];
}
}else{
if ( $Score < $NodeHash{$RefName}{$QryName}{'Score'} ) {
for ( my $Idx = 0 ; $Idx < scalar( @Columns ) ; $Idx ++ ) {
my $ColumnName = $ColumnNameArray[$Idx];
$NodeHash{$RefName}{$QryName}{$ColumnName} = $Columns[$Idx];
}
}
}
if ( ! exists ( $EdgeHash{$QryName}{$RefName} ) ) {
for ( my $Idx = 0 ; $Idx < scalar( @Columns ) ; $Idx ++ ) {
my $ColumnName = $ColumnNameArray[$Idx];
$EdgeHash{$QryName}{$RefName}{$ColumnName} = $Columns[$Idx];
}
}else{
if ( $Score < $EdgeHash{$QryName}{$RefName}{'Score'} ) {
for ( my $Idx = 0 ; $Idx < scalar( @Columns ) ; $Idx ++ ) {
my $ColumnName = $ColumnNameArray[$Idx];
$EdgeHash{$QryName}{$RefName}{$ColumnName} = $Columns[$Idx];
}
}
}
}
close IN;
return ( \%NodeHash, \%EdgeHash );
}
sub GenerateNodePairHash{
my $file=shift;
open IN1,"<$file" or die $!;
open PAIR,">ctg_pairs.txt" or die $!;
open ORI,">ctg_ctg_ori.txt" or die $!;
my %NodePairsHash = ();
#left 1 99.43 13111 R498_5995724_1/67_17121 R498_6008174_1/88_16840/0_16752 left 0 13208 16752 3863 17051 17054 QryExtend RefExtend
my %ctg_ctg_count=();
my %ctg_ctg_overlap_len=();
my %ctg_ctg_ori=();
my %ctg_ctg_chain=();
my %ctg_ctg_line=();
my %ctg_ctg_info=();
my %ctg_ctg_extend=();
while(<IN1>){
chomp;
my $line=$_;
my @content=split /\s+/,$line;
$content[5]=~/(\S+)\/0_\d+$/;
my $next=$1;
$content[5]=$next;
next if($next eq $content[4]);
my $QryName=1;
#RefPos RefStrand Identity Score RefName QryName QryPos QryStart QryEnd QryLength RefStart RefEnd RefLength QryExtend RefExtend
# next if(exists $ctg_ctg_info{ $QryStartHashArray[0]}{$QryStartHashArray[1]} && $ctg_ctg_info{ $QryStartHashArray[0]}{$QryStartHashArray[1]}{'overlap'}>=$content[3]);
$Reads_Pairs{$content[4]}{$content[0]}{$content[5]}{'S'}=$content[3]; #Score
$Reads_Pairs{$content[4]}{$content[0]}{$content[5]}{'O'}=$content[6]; #Oritention of $content[5]
$Reads_Pairs{$content[4]}{$content[0]}{$content[5]}{'E'}=$content[13]; #Extend length for $content[5]
$Reads_Pairs{$content[4]}{$content[0]}{$content[5]}{'I'}=$content[2]; #Identity of overlap
$Reads_Pairs{$content[4]}{$content[0]}{$content[5]}{'C'}=0; #chain of $content[5]
$Reads_Pairs{$content[5]}{$content[6]}{$content[4]}{'S'}=$content[3]; #Score
$Reads_Pairs{$content[5]}{$content[6]}{$content[4]}{'O'}=$content[0]; #Oritention of $content[4]
$Reads_Pairs{$content[5]}{$content[6]}{$content[4]}{'E'}=$content[14]; #Extend length for $content[4]
$Reads_Pairs{$content[5]}{$content[6]}{$content[4]}{'I'}=$content[2]; #Identity of overlap
$Reads_Pairs{$content[5]}{$content[6]}{$content[4]}{'C'}=$content[1]; #chain of $content[4]
# $ctg_ctg_extend{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}=$content[14];
# $ctg_ctg_extend{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}=$content[13];
# $ctg_ctg_extend{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}=$content[13];
# $ctg_ctg_extend{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}=$content[14];
# $ctg_ctg_count{$QryStartHashArray[0]}{$QryStartHashArray[1]}=$content[3];
# $ctg_ctg_count{$QryStartHashArray[1]}{$QryStartHashArray[0]}=$content[3];
# $ctg_ctg_overlap_len{$QryStartHashArray[0]}{$QryStartHashArray[1]}=$content[3];
# $ctg_ctg_ori{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}=$content[0];
# $ctg_ctg_ori{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}=$content[6];
# $ctg_ctg_ori{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}=$content[6];
# $ctg_ctg_ori{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}=$content[0];
# $ctg_ctg_chain{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}=$content[1];
# $ctg_ctg_chain{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}=0;
# $ctg_ctg_chain{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}=0;
# $ctg_ctg_chain{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}=$content[1];
# $ctg_ctg_line{$QryStartHashArray[0]}{$QryStartHashArray[1]}=$QryStartHashArray[0]."-".$QryStartHashArray[1]."-"."1";
# $ctg_ctg_line{$QryStartHashArray[1]}{$QryStartHashArray[0]}=$QryStartHashArray[1]."-".$QryStartHashArray[0]."-"."1";
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}{'length'}=$content[12];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}{'start'}=$content[10];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{1}{'end'}=$content[11];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}{'length'}=$content[12];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}{'start'}=$content[10];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{2}{'end'}=$content[11];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{'identity'}=$content[2];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{'overlap'}=$content[3];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{'identity'}=$content[2];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{'overlap'}=$content[3];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}{'length'}=$content[9];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}{'start'}=$content[7];
# $ctg_ctg_info{$QryStartHashArray[0]}{$QryStartHashArray[1]}{2}{'end'}=$content[8];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}{'length'}=$content[9];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}{'start'}=$content[7];
# $ctg_ctg_info{$QryStartHashArray[1]}{$QryStartHashArray[0]}{1}{'end'}=$content[8];
print ORI "$content[4]\t$content[12]\t$content[1]\t$content[0]\t$content[5]\t$content[9]\t0\t$content[6]\t$content[3]\n";
print ORI "$content[5]\t$content[9]\t0\t$content[6]\t$content[4]\t$content[12]\t$content[1]\t$content[0]\t$content[3]\n";
print PAIR "$content[4]\t$content[12]\t$content[5]\t$content[9]\t$content[3]\tNA/0_1-$content[1]-$content[10]-$content[11]-0-$content[7]-$content[8]\tNA/0_1-0-0-0-0-0\n";
print PAIR "$content[5]\t$content[9]\t$content[4]\t$content[12]\t$content[3]\tNA/0_1-0-$content[7]-$content[8]-$content[1]-$content[10]-$content[11]\tNA/0_1-0-0-0-0-0\n";
#RefPos RefStrand Identity Score RefName QryName QryPos QryStart QryEnd QryLength RefStart RefEnd RefLength
}
#NA/0_1-1---0--
=pod
foreach my $key1 (keys %ctg_ctg_info){
my $temp=$ctg_ctg_info{$key1};
foreach my $key2 (keys %$temp){
print ORI "$key1\t$ctg_ctg_info{$key1}{$key2}{1}{'length'}\t$ctg_ctg_chain{$key1}{$key2}{1}\t$ctg_ctg_ori{$key1}{$key2}{1}\t$key2\t$ctg_ctg_info{$key1}{$key2}{2}{'length'}\t$ctg_ctg_chain{$key1}{$key2}{2}\t$ctg_ctg_ori{$key1}{$key2}{2}\t$ctg_ctg_count{$key1}{$key2}\n";
print PAIR "$key1\t$ctg_ctg_info{$key1}{$key2}{1}{'length'}\t$key2\t$ctg_ctg_info{$key1}{$key2}{2}{'length'}\t$ctg_ctg_count{$key1}{$key2}\tNA/0_1-$ctg_ctg_chain{$key1}{$key2}{1}-$ctg_ctg_info{$key1}{$key2}{1}{'start'}-$ctg_ctg_info{$key1}{$key2}{1}{'end'}-$ctg_ctg_chain{$key1}{$key2}{2}-$ctg_ctg_info{$key1}{$key2}{2}{'start'}-$ctg_ctg_info{$key1}{$key2}{2}{'end'}\tNA/0_1-0-0-0-0-0\n";
}
}
=cut
close(PAIR);
close(ORI);
return(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line, \%ctg_ctg_extend, \%ctg_ctg_info);
}
#&Finding_best_pathway(\%ctg_ctg_count, \%ctg_ctg_overlap_len, \%ctg_ctg_ori, \%ctg_ctg_chain, \%ctg_ctg_line, \%NodePairsHash );
sub Finding_best_pathway{
my $ctg_pair_count = shift;
my $ctg_ctg_overlap = shift;
my $ctg_ori = shift;
my $ctg_chain = shift;
my $ctg_line =shift ;
# my $PairsHash = shift;
my %ctg_ctg_count = %{$ctg_pair_count};
my %ctg_ctg_overlap = %{$ctg_ctg_overlap};
my %ctg_ctg_ori = %{$ctg_ori};
my %ctg_ctg_chain = %{$ctg_chain};
my %ctg_ctg_line = %{$ctg_line};
# my %NodePairsHash = %{$PairsHash};
my %All_existed_clusters=(); #$All_existed_clusters
my @cluster_line=(); #ctg clusters
open OUT,">ctg_clusters.txt" or die $!;
#首先判断一对contig中，是否有一个contig是最好的，如果两个contig都不是最好的，过；否则延伸
my %existed_pairs=();
my %all_existed_ctgs=();
my %all_existed_pairs=();
foreach my $left_ctg (keys %ctg_ctg_line){
my $temp_ctg=$ctg_ctg_line{$left_ctg};
foreach my $right_ctg (keys %$temp_ctg){
next if(exists $existed_pairs{$left_ctg}{$right_ctg});
my $left_ctg_order=1;
my $right_ctg_order=1;
################ 判断左边contig是否为其同方向中最好的 ##############################################
=pod
foreach my $left_key1 (keys %ctg_ctg_line){
my $left_temp_ctg=$ctg_ctg_line{$left_key1};
foreach my $left_key2 (keys %$left_temp_ctg){
next if($left_ctg eq $left_key1 && $right_ctg eq $left_key2);
if($left_ctg eq $left_key2){
if($ctg_ctg_ori{$left_key1}{$left_key2}{2} eq $ctg_ctg_ori{$left_ctg}{$right_ctg}{1}){
if($ctg_ctg_count{$left_ctg}{$right_ctg}<$ctg_ctg_count{$left_key1}{$left_key2}){
$left_ctg_order++;
}
elsif($ctg_ctg_count{$left_ctg}{$right_ctg}==$ctg_ctg_count{$left_key1}{$left_key2}){
if($ctg_ctg_overlap{$left_ctg}{$right_ctg}<$ctg_ctg_overlap{$left_key1}{$left_key2}){
$left_ctg_order++;
}
}
}
}
}
}
=cut
my $left_add=$ctg_ctg_line{$left_ctg};
foreach my $left_key (keys %$left_add){
next if($left_key eq $right_ctg);
if($ctg_ctg_ori{$left_ctg}{$left_key}{1} eq $ctg_ctg_ori{$left_ctg}{$right_ctg}{1}){
if($ctg_ctg_count{$left_ctg}{$right_ctg}<$ctg_ctg_count{$left_ctg}{$left_key}){
$left_ctg_order++;
}
elsif($ctg_ctg_count{$left_ctg}{$right_ctg}==$ctg_ctg_count{$left_ctg}{$left_key}){
if($ctg_ctg_overlap{$left_ctg}{$right_ctg}<$ctg_ctg_overlap{$left_ctg}{$left_key}){
$left_ctg_order++;
}
}
}
}
##############判断右边contig是否为其同方向中最好的contig #########################################
=pod
foreach my $right_key1 (keys %ctg_ctg_line){
my $right_temp_ctg=$ctg_ctg_line{$right_key1};
foreach my $right_key2 (keys %$right_temp_ctg){
next if($left_ctg eq $right_key1 && $right_ctg eq $right_key2);
if($right_ctg eq $right_key2){
if($ctg_ctg_ori{$right_key1}{$right_key2}{2} eq $ctg_ctg_ori{$left_ctg}{$right_ctg}{2}){
if($ctg_ctg_count{$left_ctg}{$right_ctg}<$ctg_ctg_count{$right_key1}{$right_key2}){
$right_ctg_order++;
}
elsif($ctg_ctg_count{$left_ctg}{$right_ctg}==$ctg_ctg_count{$right_key1}{$right_key2}){
if($ctg_ctg_overlap{$left_ctg}{$right_ctg}<$ctg_ctg_overlap{$right_key1}{$right_key2}){
$right_ctg_order++;
}
}
}
}
}
}
=cut
my $right_add=$ctg_ctg_line{$right_ctg};
foreach my $right_key (keys %$right_add){
next if($right_key eq $left_ctg);
if($ctg_ctg_ori{$right_ctg}{$right_key}{1} eq $ctg_ctg_ori{$left_ctg}{$right_ctg}{2}){
if($ctg_ctg_count{$left_ctg}{$right_ctg}<$ctg_ctg_count{$right_ctg}{$right_key}){
$right_ctg_order++;
}
elsif($ctg_ctg_count{$left_ctg}{$right_ctg}==$ctg_ctg_count{$right_ctg}{$right_key}){
if($ctg_ctg_overlap{$left_ctg}{$right_ctg}<$ctg_ctg_overlap{$right_ctg}{$right_key}){
$right_ctg_order++;
}
}
}
}
next if($right_ctg_order>1 || $left_ctg_order>1);
next if(exists $all_existed_pairs{$left_ctg}{$right_ctg});
next if(exists $all_existed_ctgs{$left_ctg} || exists $all_existed_ctgs{$right_ctg});
$all_existed_pairs{$left_ctg}{$right_ctg}=0;
$all_existed_ctgs{$left_ctg}=0;
$all_existed_ctgs{$right_ctg}=0;
# print "$left_ctg\t$right_ctg\n";
#################### 结束判断 ################################################################
################### 以上面找到的一对contig为起始 分别左右延伸寻找最好的contig ################
my @extend_line=();
push(@extend_line,$left_ctg);
push(@extend_line,$right_ctg);
my $left_extend=$left_ctg;
my $right_extend=$right_ctg;
my %existed_ctg=();
$existed_ctg{$left_extend}=0;
$existed_ctg{$right_extend}=0;
my %extended_ctg=();
my %existed_ctg_ori=();
$existed_ctg_ori{$left_ctg}=$ctg_ctg_ori{$left_ctg}{$right_ctg}{1};
$existed_ctg_ori{$right_ctg}=$ctg_ctg_ori{$left_ctg}{$right_ctg}{2};
my $left_extend_ctg="1";
my $left_extend_count=0;
my $left_overlap=0;
while($left_extend_ctg ne ""){
$left_extend_ctg="";
$left_extend_count=0;
$left_overlap=0;
$left_extend=$extend_line[0];
# last if(exists $extended_ctg{$left_extend}); #判断该contig是否已经延伸过
$extended_ctg{$left_extend}=0;
foreach my $key1 (keys %ctg_ctg_line){
my $temp=$ctg_ctg_line{$key1};
foreach my $key2 (keys %$temp){
if($key2 eq $left_extend){
if($ctg_ctg_ori{$key1}{$key2}{2} ne $ctg_ctg_ori{$left_extend}{$extend_line[1]}{1}){
if($ctg_ctg_count{$key1}{$key2}>$left_extend_count){
$left_extend_ctg=$key1;
$left_extend_count=$ctg_ctg_count{$key1}{$key2};
$left_overlap=$ctg_ctg_overlap{$key1}{$key2};
}
elsif($ctg_ctg_count{$key1}{$key2}==$left_extend_count){
if($ctg_ctg_overlap{$key1}{$key2}>$left_overlap){
$left_extend_ctg=$key1;
$left_extend_count=$ctg_ctg_count{$key1}{$key2};
$left_overlap=$ctg_ctg_overlap{$key1}{$key2};
}
}
}
}
}
}
my $temp=$ctg_ctg_line{$left_extend};
foreach my $key10 (keys %$temp ){
if($ctg_ctg_ori{$left_extend}{$key10}{1} ne $ctg_ctg_ori{$left_extend}{$extend_line[1]}{1}){
if($ctg_ctg_count{$left_extend}{$key10}>$left_extend_count){
$left_extend_ctg=$key10;
$left_extend_count=$ctg_ctg_count{$left_extend}{$key10};
$left_overlap=$ctg_ctg_overlap{$left_extend}{$key10};
}
elsif($ctg_ctg_count{$left_extend}{$key10}==$left_extend_count){
if($ctg_ctg_overlap{$left_extend}{$key10}>$left_overlap){
$left_extend_ctg=$key10;
$left_extend_count=$ctg_ctg_count{$left_extend}{$key10};
$left_overlap=$ctg_ctg_overlap{$left_extend}{$key10};
}
}
}
}
if(exists $all_existed_ctgs{$left_extend_ctg}){
last;
}
if(exists $existed_ctg{$left_extend_ctg}){
$left_extend_ctg="";
}
elsif(!exists $existed_ctg{$left_extend_ctg} && $left_extend_ctg ne ""){
unshift(@extend_line,$left_extend_ctg);
$all_existed_ctgs{$left_extend_ctg}=0;
$all_existed_pairs{$left_extend_ctg}{$left_extend}=0;
$existed_pairs{$left_extend_ctg}{$left_extend}=0;
$existed_pairs{$left_extend_ctg}{$left_extend}=0;
}
$existed_ctg{$left_extend_ctg}=0;
}
###################### 开始延伸右边 #############################################################
my $right_extend_ctg="1";
my $right_extend_count=0;
my $right_overlap=0;
while($right_extend_ctg ne ""){
$right_extend_ctg="";
$right_extend_count=0;
$right_overlap=0;
$right_extend=$extend_line[-1];
# last if(exists $extended_ctg{$right_extend});
$extended_ctg{$right_extend}=0;
foreach my $key1 (keys %ctg_ctg_line){
my $temp=$ctg_ctg_line{$key1};
foreach my $key2 (keys %$temp){
if($key2 eq $right_extend){
if($ctg_ctg_ori{$key1}{$key2}{2} ne $ctg_ctg_ori{$right_extend}{$extend_line[-2]}{1}){
if($ctg_ctg_count{$key1}{$key2}>$right_extend_count){
$right_extend_ctg=$key1;
$right_extend_count=$ctg_ctg_count{$key1}{$key2};
$right_overlap=$ctg_ctg_overlap{$key1}{$key2};
}
elsif($ctg_ctg_count{$key1}{$key2}==$right_extend_count){
if($ctg_ctg_overlap{$key1}{$key2}>$right_overlap){
$right_extend_ctg=$key1;
$right_extend_count=$ctg_ctg_count{$key1}{$key2};
$right_overlap=$ctg_ctg_overlap{$key1}{$key2};
}
}
}
}
}
}
my $temp=$ctg_ctg_line{$right_extend};
foreach my $key1 (keys %$temp ){
next if($key1 eq $extend_line[-2]);
if($ctg_ctg_ori{$right_extend}{$key1}{1} ne $ctg_ctg_ori{$right_extend}{$extend_line[-2]}{1}){
if($ctg_ctg_count{$right_extend}{$key1}>$right_extend_count){
$right_extend_ctg=$key1;
$right_extend_count=$ctg_ctg_count{$right_extend}{$key1};
$right_overlap=$ctg_ctg_overlap{$right_extend}{$key1};
}
elsif($ctg_ctg_count{$right_extend}{$key1}==$right_extend_count){
if($ctg_ctg_overlap{$right_extend}{$key1}>$right_overlap){
$right_extend_ctg=$key1;
$right_extend_count=$ctg_ctg_count{$right_extend}{$key1};
$right_overlap=$ctg_ctg_overlap{$right_extend}{$key1};
}
}
}
}
if(exists $all_existed_ctgs{$right_extend_ctg}){
last;
}
if(exists $existed_ctg{$right_extend_ctg}){
$right_extend_ctg="";
}
elsif(!exists $existed_ctg{$right_extend_ctg} && $right_extend_ctg ne ""){
push(@extend_line,$right_extend_ctg);
$all_existed_ctgs{$right_extend_ctg}=0;
$all_existed_pairs{$right_extend}{$right_extend_ctg}=0;
$existed_pairs{$right_extend}{$right_extend_ctg}=0;
$existed_pairs{$right_extend_ctg}{$right_extend}=0;
}
$existed_ctg{$right_extend_ctg}=0;
}
my $ctg_cluster=$extend_line[0];
for(my $i=1;$i<@extend_line;$i++){
$ctg_cluster=$ctg_cluster."-".$extend_line[$i];
}
# print "$left_ctg $right_ctg----$ctg_cluster\n";
my $sign=0;
for(my $i=0;$i<@cluster_line;$i++){
if($cluster_line[$i]=~/$ctg_cluster/){
$sign=1;
}
elsif($ctg_cluster=~/$cluster_line[$i]/){
$cluster_line[$i]=$ctg_cluster;
$sign=1;
}
else{
my @content=split "-",$ctg_cluster;
my $reverse=join ("-",reverse(@content));
if($reverse=~/$cluster_line[$i]/){
$cluster_line[$i]=$reverse;
$sign=1;
}
elsif($cluster_line[$i]=~/$reverse/){
$sign=1;
}
}
}
################# 检查所有已经找到的通路中是否有包含当前通路中所有contig的通路 ##############
for(my $j=0;$j<@cluster_line;$j++){
$cluster_line[$j]=~s/^\s+|\s+$//g;
my @target_ctg=split "-",$cluster_line[$j];
my %ctg_target=();
my %ctg_query=();
for(my $target=0;$target<@target_ctg;$target++){
$ctg_target{$target_ctg[$target]}=0;
}
for(my $query=0;$query<@extend_line;$query++){
next if($extend_line[$query] eq "");
$ctg_query{$extend_line[$query]}=0;
}
my $target_sign=0;
foreach my $target_key(keys %ctg_target){
if(!exists $ctg_query{$target_key}){
$target_sign=1;
}
}
if($target_sign==0){
$cluster_line[$j]=$ctg_cluster;
$sign=1;
}
my $query_sign=0;
foreach my $query_key(keys %ctg_query){
if(!exists $ctg_target{$query_key}){
$query_sign=1;
}
}
if($query_sign==0){
$sign=1;
}
# print "1----$ctg_cluster\n2----$cluster_line[$j]\n3----$target_sign\t$query_sign\n";
}
############################ end #######################################################
if($sign==0){
if(!exists $All_existed_clusters{$ctg_cluster}){
$ctg_cluster=~s/^\s+|\s+$//g;
push(@cluster_line,$ctg_cluster);
$All_existed_clusters{$ctg_cluster}=0;
}
}
}
}
# print "@cluster_line\n";
my %hash=();
my @Final_cluster=();
for(my $i=0;$i<@cluster_line;$i++){
my @content=split "-",$cluster_line[$i];
next if(exists $hash{$cluster_line[$i]});
$hash{$cluster_line[$i]}=0;
push (@Final_cluster,$cluster_line[$i]);
for(my $j=0;$j<@content;$j++){
print OUT "$content[$j] ";
}
print OUT "\n";
}
close(OUT);
return (@Final_cluster);
}
sub draw_ctg_clusters{
my $info=shift;
my @ctg_cluster=@{$info};
# my $ClusterGraph = Graph::Easy->new( undirected => 1 );
my %existed_ctg=();
# print "@ctg_cluster\n";
open CLUSTER,">cluster_ori.txt" or die $!;
for(my $i=0;$i<@ctg_cluster;$i++){
my @content=split "-",$ctg_cluster[$i];
=pod
for(my $j=0;$j<@content;$j++){
next if(exists $existed_ctg{$content[$j]});
$EasyGraph -> add_node( $content[$j] );
}
=cut
for(my $j=0;$j<@content-1;$j++){
my @infor=split "-",$ctg_ctg_line{$content[$j]}{$content[$j+1]};
print CLUSTER "$content[$j] $ctg_ctg_chain{$content[$j]}{$content[$j+1]}{1} $ctg_ctg_ori{$content[$j]}{$content[$j+1]}{1} $ctg_ctg_chain{$content[$j]}{$content[$j+1]}{2} $ctg_ctg_ori{$content[$j]}{$content[$j+1]}{2} ";
}
print CLUSTER "$content[-1]\n";
}
# &drawEasyGraph ( $ClusterGraph , "ctg_cluster" , '01' );
}
=pod
open OUT1,">pairs.txt" or die $!;
foreach my $key1 (keys %NodePairsHash){
my $temp=$NodePairsHash{$key1};
my @content=split "-",$key1;
foreach my $pacbio (keys %$temp){
print OUT1 "$content[0] $NodePairsHash{$key1}{$pacbio}{'First'}{'RefPos'} $NodePairsHash{$key1}{$pacbio}{'First'}{'RefStrand'} $NodePairsHash{$key1}{$pacbio}{'First'}{'Identity'} $NodePairsHash{$key1}{$pacbio}{'First'}{'RefStart'} $NodePairsHash{$key1}{$pacbio}{'First'}{'RefEnd'} $NodePairsHash{$key1}{$pacbio}{'First'}{'RefLength'}-----$content[1] $NodePairsHash{$key1}{$pacbio}{'Next'}{'RefPos'} $NodePairsHash{$key1}{$pacbio}{'Next'}{'RefStrand'} $NodePairsHash{$key1}{$pacbio}{'Next'}{'Identity'} $NodePairsHash{$key1}{$pacbio}{'Next'}{'RefStart'} $NodePairsHash{$key1}{$pacbio}{'Next'}{'RefEnd'} $NodePairsHash{$key1}{$pacbio}{'Next'}{'RefLength'}\n";
}
}
=cut
sub Finding_All_pathway{
my $ctg_pair_count = shift;
my $ctg_ctg_overlap = shift;
my $ctg_ori = shift;
my $ctg_chain = shift;
my $ctg_line =shift ;
my $SEPoint=shift;
# my $PairsHash = shift;
# $Pair_Graph
my %ctg_ctg_count = %{$ctg_pair_count};
my %ctg_ctg_overlap = %{$ctg_ctg_overlap};
my %ctg_ctg_ori = %{$ctg_ori};
my %ctg_ctg_chain = %{$ctg_chain};
my %ctg_ctg_line = %{$ctg_line};
my %Scaffold_Contig_SEPoint = %{ $SEPoint};
# my %NodePairsHash = %{$PairsHash};
my %All_existed_clusters=(); #$All_existed_clusters
my @cluster_line=(); #ctg clusters
open OUT,">ctg_clusters.txt" or die $!;
print "Finding_All_Pathway\n";
my @Final_Cluster=();
#首先判断一对contig中，是否有一个contig是最好的，如果两个contig都不是最好的，过；否则延伸
my %existed_pairs=();
my %all_existed_ctgs=();
my %all_existed_pairs=();
#以Scaffold为单位，两两Contig之间寻找通路
foreach my $Scaffold (sort {$a cmp $b} keys %Scaffold_Contig_SEPoint){
my $temp_scaffold=$Scaffold_Contig_SEPoint{$Scaffold};
foreach my $scaffold_contig (sort {$a<=>$b} keys %$temp_scaffold){
my %All_Path=();
my $First_Scaffold_Contig=$Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'};
#比对到前面Ctg末尾的Pacbio
my $next_contig=$scaffold_contig+1;
last if(!exists $Scaffold_Contig_SEPoint{$Scaffold}{$next_contig});
my $Second_Scaffold_Contig=$Scaffold_Contig_SEPoint{$Scaffold}{$next_contig}{'Head'};
#比对到后面Ctg开头的Pacbio
#利用Graph：Pair_Graph存储的信息判断两个Contig之间是否存在通路
foreach my $First_Pacbio (keys %$First_Scaffold_Contig){
# my %exists_Pacbio=();
foreach my $Second_Pacbio (keys %$Second_Scaffold_Contig){
# next if(exists $exists_Pacbio{$Second_Pacbio});
# if($Pair_Graph->is_reachable($First_Pacbio,$Second_Pacbio)){
# print "$First_Pacbio $Second_Pacbio reachable\n";
if($Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'}{$First_Pacbio}{0}==0){ #链为正，right延伸
my @neighbors=();
# $Pair_Graph->neighbours($First_Pacbio);
last if(!@neighbors);
#存储与起始pacbio，延伸方向一致的pacbio对
for(my $i=0;$i<@neighbors;$i++){
next if($First_Pacbio eq $neighbors[$i]);
if($ctg_ctg_ori{$First_Pacbio}{$neighbors[$i]}{1} eq "right"){
my $current_path=$First_Pacbio."-".$neighbors[$i];
$All_Path{$current_path}{$First_Pacbio}=1;
$All_Path{$current_path}{$neighbors[$i]}=2;
$All_Path{$current_path}{'Total'}=2;
$All_Path{$current_path}{'Extend'}=1; #1表示可延伸，0表示该通路不可延伸
}
}
#开始向右延伸pacbio;
#如果在同一条通路中遇到相同的节点，则该通路延伸停止；否则一直延伸直到无可延伸的pacbio,或者延伸的pacbio在下一个Contig的开头
my $If_Extend=1;
while($If_Extend != 0){
$If_Extend=0;
foreach my $path (keys %All_Path){
my @Pacbio_In_Path=split /-/,$path;
my $temp_path=$ctg_ctg_ori{$Pacbio_In_Path[-1]};
# next if($All_Path{$path}{'Extend'}==0);
foreach my $extend_pacbio (keys %$temp_path){
next if($extend_pacbio eq $Pacbio_In_Path[-2]);
if($ctg_ctg_ori{$Pacbio_In_Path[-2]}{$Pacbio_In_Path[-1]}{2} ne $ctg_ctg_ori{$Pacbio_In_Path[-1]}{$extend_pacbio}{1}){
next if(exists $All_Path{$path}{$extend_pacbio});
#如果该通路中已经包含该pacbio，则停止对该通路的延伸
my $path_extended=$path."-".$extend_pacbio;
$All_Path{$path_extended}{'Total'}=$All_Path{$path}{'Total'}+1;
$All_Path{$path_extended}{$extend_pacbio}=$All_Path{$path_extended}{'Total'};
# if(exists $Scaffold_Contig_SEPoint{$Scaffold}{$next_contig}{'Head'}{$extend_pacbio}){
# $All_Path{$path_extended}{'Extend'}=0;
# }
$If_Extend=1;
}
}
if($If_Extend==1){
delete ($All_Path{$path});
}
elsif($If_Extend==0){
# $All_Path{$path}{'Extend'}=0;
}
}
}
foreach my $Final_Path (keys %All_Path){
push(@Final_Cluster,$Final_Path);
my @content=split /-/,$Final_Path;
print OUT "@content\n";
}
%All_Path=();
}
##对于正链比对到前一个Ctg上pacbio，向右延伸结束
##对于反链比对到前一个Ctg末尾的pacbio，开始向该pacbio左端延伸
else{ #链为负，left延伸
my @neighbors=();
# $Pair_Graph->neighbours($First_Pacbio);
last if(!@neighbors);
for(my $i=0;$i<@neighbors;$i++){
next if($First_Pacbio eq $neighbors[$i]);
if($ctg_ctg_ori{$First_Pacbio}{$neighbors[$i]}{1} eq "left"){
my $current_path=$First_Pacbio."-".$neighbors[$i];
$All_Path{$current_path}{$First_Pacbio}=1;
$All_Path{$current_path}{$neighbors[$i]}=2;
$All_Path{$current_path}{'Total'}=2;
$All_Path{$current_path}{'Extend'}=1;
}
}
my $If_Extend=1;
while($If_Extend != 0){
$If_Extend=0;
foreach my $path (keys %All_Path){
my @Pacbio_In_Path=split /-/,$path;
my $temp_path=$ctg_ctg_ori{$Pacbio_In_Path[-1]};
next if($All_Path{$path}{'Extend'}==0);
foreach my $extend_pacbio (keys %$temp_path){
next if($extend_pacbio eq $Pacbio_In_Path[-2]);
if($ctg_ctg_ori{$Pacbio_In_Path[-2]}{$Pacbio_In_Path[-1]}{2} ne $ctg_ctg_ori{$Pacbio_In_Path[-1]}{$extend_pacbio}{1}){
next if(exists $All_Path{$path}{$extend_pacbio});
my $path_extended=$path."-".$extend_pacbio;
$All_Path{$path_extended}{'Total'}=$All_Path{$path}{'Total'}+1;
$All_Path{$path_extended}{$extend_pacbio}=$All_Path{$path_extended}{'Total'};
if(exists $Scaffold_Contig_SEPoint{$Scaffold}{$next_contig}{'Head'}{$extend_pacbio}){
# $All_Path{$path_extended}{'Extend'}=0;
}
$If_Extend=1;
}
}
if($If_Extend==1){
delete ($All_Path{$path});
}
elsif($If_Extend==0){
# $All_Path{$path}{'Extend'}=0;
}
}
}
}
foreach my $Final_Path (keys %All_Path){
push(@Final_Cluster,$Final_Path);
my @content=split /-/,$Final_Path;
print OUT "@content\n";
}
%All_Path=();
# }
}
}
}
}
close(OUT);
return (@Final_Cluster);
}
sub Finding_Best_Pathway{
my $ctg_pair_count = shift;
my $ctg_ctg_overlap = shift;
my $ctg_ori = shift;
my $ctg_chain = shift;
my $ctg_line =shift ;
my $SEPoint=shift;
my %ctg_ctg_count = %{$ctg_pair_count};
my %ctg_ctg_overlap = %{$ctg_ctg_overlap};
my %ctg_ctg_ori = %{$ctg_ori};
my %ctg_ctg_chain = %{$ctg_chain};
my %ctg_ctg_line = %{$ctg_line};
my %Scaffold_Contig_SEPoint = %{ $SEPoint};
my %All_existed_clusters=(); #$All_existed_clusters
my @cluster_line=(); #ctg clusters
open OUT,">ctg_clusters.txt" or die $!;
open CLUSTER,">cluster_ori.txt" or die $!;
#首先判断一对contig中，是否有一个contig是最好的，如果两个contig都不是最好的，过；否则延伸
my %existed_pairs=();
my %all_existed_ctgs=();
my %all_existed_pairs=();
my $Bestn=1;
print OUT "Real Starting Extending\n";
my $sign=0;
################################ test #############################################
open TEST,">test.txt" or die $!;
=pod
foreach my $key (keys %ctg_ctg_count){
my $temp=$ctg_ctg_count{$key};
my @num=keys %$temp;
my $total=@num;
print TEST "$key $total\n";
}
close(TEST);
=cut
############################### test ################################################
foreach my $Scaffold (sort {$a cmp $b} keys %Scaffold_Contig_SEPoint){
# next if($Scaffold ne "Super-Scaffold_119");
my $time=&gettime("yyyy-mm-dd hh:mi:ss");
print TEST "$time\n";
print TEST "Begining Super-Scaffold_119\n";
close(TEST);
open TEST,">>test.txt" or die $!;
my $temp_scaffold=$Scaffold_Contig_SEPoint{$Scaffold};
foreach my $scaffold_contig (sort {$a<=>$b} keys %$temp_scaffold){
my $First_Scaffold_Contig=$Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'};
my $next_contig=$scaffold_contig+1;
last if(!exists $Scaffold_Contig_SEPoint{$Scaffold}{$next_contig});
$sign++;
my $First_Contig=$Scaffold.".".$scaffold_contig;
my $Second_Contig=$Scaffold.".".$next_contig;
my $Real_Gap=$Contig_Gap_Length{$First_Contig}{$Second_Contig};
my $Second_Scaffold_Contig=$Scaffold_Contig_SEPoint{$Scaffold}{$next_contig}{'Head'};
my %Bestn_PathWay=();
print TEST "Begining $scaffold_contig\n";
close(TEST);
open TEST,">>test.txt" or die $!;
foreach my $First_Pacbio (keys %$First_Scaffold_Contig){
my $Start_Ori="";
if($Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'}{$First_Pacbio}{0}==0){
$Start_Ori="right";
}
elsif($Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'}{$First_Pacbio}{0}==1){
$Start_Ori="left";
}
my $First_Temp=$Reads_Pairs{$First_Pacbio}{$Start_Ori};
my $Current_Best=0;
my %All_Path=();
foreach my $Query (sort {$Reads_Pairs{$First_Pacbio}{$Start_Ori}{$b}{'S'} <=> $Reads_Pairs{$First_Pacbio}{$Start_Ori}{$a}{'S'}} keys %$First_Temp){
last if($Current_Best>=$Bestn);
next if($First_Pacbio eq $Query);
if(($Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'}{$First_Pacbio}{0}==0 && $Start_Ori eq "right") || (($Scaffold_Contig_SEPoint{$Scaffold}{$scaffold_contig}{'Tail'}{$First_Pacbio}{0}==1 && $Start_Ori eq "left"))){
my $current_path=$First_Pacbio."-".$Query;
if(exists $Scaffold_Contig_SEPoint{$Scaffold}{$next_contig}{'Head'}{$Query}){
$All_Path{$current_path}=1;
}
else{