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Code.S3.identify.MDS.structures.pl
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Code.S3.identify.MDS.structures.pl
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# Merge intergrated MDSs
# load options and prepare output path
use Getopt::Long;
use File::Basename;
use strict;
my $outPath="./Output";
my $MACfile;
my $MICfile;
my $telo_file;
my $input_mode=2;
my $inPut_File;
our $Pident_limit||=97;
our $Evalue_limit||=1E-10;
our $max_overlaps||=0.05; # percentage of whole MDS
GetOptions(
'mac=s' =>\$MACfile,
'mic=s' =>\$MICfile,
'telo=s' =>\$telo_file,
'pi=s' =>\$Pident_limit,
'ev=s' =>\$Evalue_limit,
'mo=s' =>\$max_overlaps,
'o=s' =>\$outPath,
'blast=s' => \$inPut_File,
);
die "[Usage] perl $0 -mac MAC.telomere-trimmed.fa -telo MAC.telomeres.tsv -mic MIC.fa -blast blast.outfmt10.csv\n".
"\t -mac: MAC genome assembly without any telomeres. This file should be used for BLAST-searching.\n".
"\t -telo: a tab-delimited file recording the telomeres count and size for each MAC contig. Four columns required: mac_id<tab>telomere_count<tab>5p_size<tab>3p_size\n".
"\t -mic: MIC genome assembly. This file should be used for BLAST-searching.\n".
"\t -blast: the 2-step BLAST-searching results in a comma-delimited file\n".
"\n\toptions:\n".
"\t -o: path of outputs. [Output]\n".
"\t -pi: minimum allowable percentage of identical matches for BLAST-HSPs [97]\n".
"\t -ev: maximum allowable expect value for BLAST-HSPs [1e-10]\n".
"\t -mo: maximum allowable overlaps between two adjacent MDSs on both MAC and MIC contigs. [0.05, stands for 5% of the MDSs]\n".
"\t Such overlaps may be caused by insufficient assembly quality. If two MDSs overlap in both MAC and MIC contigs, they will be merged if the overlap is less than the requirement. \n"
unless(-s $MACfile and -s $telo_file and -s $MICfile and -s $inPut_File);
chop $outPath if($outPath=~/\/$/);
# Check and create working directories
mkdir $outPath or die "Fail to creat the directory $outPath\n" unless(-e $outPath);
mkdir "$outPath/Progess/" or die "Fail to creat the directory 'Progess'\n" unless( -e "$outPath/Progess/");
mkdir "$outPath/MAC.annotation/" or die "Fail to creat the directory 'MAC'\n" unless(-e "$outPath/MAC.annotation/");
mkdir "$outPath/MIC.annotation/" or die "Fail to creat the directory 'MIC'\n" unless (-e "$outPath/MIC.annotation/");
# Creat output files
open Error_log,">","$outPath/Progess/Process.err" or die $!;
open Canonical_section,">","$outPath/Progess/middle.Canonically_Merged_Records.csv" or die $!;
# Get basename
my @suffixlist=qw(.fa .fas .fasta);
my ($MAC_basename, $MAC_inpath, $MAC_suffix)=fileparse($MACfile, @suffixlist);
my ($MIC_basename, $MIC_inpath, $MIC_suffix)=fileparse($MICfile, @suffixlist);
# time recording
my $time_start=time();
local $|=1;
# load MAC genome and MIC genome
our %MAChash;
our %MAClen;
our %MAC_scaff_codes;
our %MIChash;
our %MIClen;
our %MIC_scaff_codes;
&load_genome($MACfile,$MICfile) ;
# stat telomeres of each contig in both Genomes ================================================================================
our %MAC_tel_5;
our %MAC_tel_3;
&stat_MAC_tels($telo_file);
# prepare hash
our %step01_Blast_result;
our %step01_MICbased_Blast_result;
our %MAC_blast_coverage_statistics;
our %direction_of_MIC;
our %MICbased_elim1st_Blast_result;
our %step01_HSP_list;
our %MACbased_canonical_Merge_record;
our %MICbased_canonical_Merge_record;
our %canonical_merged_MAC_MIC_combinations;
our %step02_Tyically_Merged_HSP_List;
our %MAChsp_TMR;
# load blast results
if($input_mode==1){
# deprecated
}elsif($input_mode==2){
print " Loading Blast Result ...\n";
open Blast_Qualified_result,">","$outPath/Progess/Blast.qualified.outfmt10" or die $!;
my ($tmp,$Qualified_blastInf)=load_Blast_out10($input_mode,$inPut_File,\%step01_Blast_result,\%step01_MICbased_Blast_result,\%direction_of_MIC,\%MAC_blast_coverage_statistics);
print Blast_Qualified_result $Qualified_blastInf;
}
print " Building HSP list:\t\t[ ";
my $process=0;
for my $MACname (sort keys %step01_Blast_result){
$process++;
print "=" if( $process%((keys %step01_Blast_result)/20)==0);
for my $MICname (sort keys %{$step01_Blast_result{$MACname}}){
# [c1-Generate HSP_list with Primary elimination (e.g. same HSPs and overlapped HSPs)]
for my $MACinfo( sort {${$step01_Blast_result{$MACname}{$MICname}}{$a}<=>${$step01_Blast_result{$MACname}{$MICname}}{$b} } keys %{$step01_Blast_result{$MACname}{$MICname}}){
my @inf=split /,/,$MACinfo;
my $MIClen=$MIClen{$MICname};
my ($MACstart,$MACend,$MICstart,$MICend)=@inf[5,6,7,8];
anchor_1:
my $dealted=0;
# (1) merge same hits, may caused by 2-step blast
if(exists ${$step01_HSP_list{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"}){
next;
}
# (2) merge nested hits, may caused by 2-step blast
for my $position(sort {$a cmp $b} keys %{$step01_HSP_list{$MACname}{$MICname}}){
my ($covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend)=split /,/,$position;
if(($covered_MACstart<$MACstart and $MACend<=$covered_MACend) or ($covered_MACstart<=$MACstart and $MACend<$covered_MACend) ){
&Delete_MAC_MIC_pos($MACname,$MICname,"$MACstart,$MACend,$MICstart,$MICend",\%step01_HSP_list);
$dealted=1;
last;
}
elsif( ($MACstart<$covered_MACstart and $MACend>=$covered_MACend) or ($MACstart<=$covered_MACstart and $MACend>$covered_MACend) ){
&Delete_MAC_MIC_pos($MACname,$MICname,"$covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend",\%step01_HSP_list);
$dealted=2;
last;
}
}
next if($dealted==1);
goto anchor_1 if($dealted==2);
# (3) keep the HSP
($dealted==0)? ${$step01_HSP_list{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"}=$MACinfo : goto Check_again ; #unnecessary but kept
}
# [c1-Complete : Generate step01_HSP_list]
# [c2-canonical merge]
for my $coordinate (sort by_MAC_hsp_coordinate keys %{$step01_HSP_list{$MACname}{$MICname}}){
my $HSP_infos=$step01_HSP_list{$MACname}{$MICname}{$coordinate};
my $MIClen=$MIClen{$MICname};
my ($MACstart,$MACend,$MICstart,$MICend,$strand)=(split /,/,$HSP_infos)[5,6,7,8,12];
$MICbased_elim1st_Blast_result{$MICname}{$step01_HSP_list{$MACname}{$MICname}{$coordinate}}="$MICstart.$MICend";
anchor_2:
my $dealted=0;
for my $covered_position(sort by_MAC_hsp_coordinate keys %{$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}}){
my $covered_HSP_infos=$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}{$covered_position};
my @inf=split /,/,$covered_HSP_infos;
my ($covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend,$covered_strand)=@inf[5,6,7,8,12];
if( §ions_separate_or_not($MICname,$MACname,$MICstart,$MICend,$MACstart,$MACend,$covered_MICstart,$covered_MICend,$covered_MACstart,$covered_MACend,\%MICbased_canonical_Merge_record) eq "Y" ){
# 5'___________________________|_______________________/_____|______________________/___________________________________3'
# MAC: covered_MACstart MACstart covered_MACend MACend
#
# 5'____________________|_______________________|__________________/_________________________/__________________________3'
# MIC: covered_MICstart/end MICend/start covered_MICstart/end MICend/start
if($covered_MACstart<$MACstart and -1<=$covered_MACend-$MACstart and $covered_MACend<$MACend){
my ($new_MICstart,$new_MICend,$new_Strand)=get_NewStartAndEnd($MICstart,$MICend,$strand,$covered_MICstart,$covered_MICend,$covered_strand,$MACname,$MICname);
unless($new_MICstart>0 and $new_MICend>0){
my $error_inf="\n [Error][incomplete loci] adjusted MIC position are $new_MICstart -> $new_MICend\n";
print $error_inf;
print Error_log $error_inf;
next ;
}
my $records="$MACname,$MICname,s1,$covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend,$covered_strand,s2,$MACstart,$MACend,$MICstart,$MICend,$strand";
if(exists ${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{"$covered_MACstart,$MACend,$new_MICstart,$new_MICend"}){
print "Conflict MAC canonical merging: \nnow: ".$records."\n".${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{"$covered_MACstart,$MACend,$new_MICstart,$new_MICend"}."\n";
}elsif(exists ${$MICbased_canonical_Merge_record{$MICname}{$MACname}}{"$new_MICstart,$new_MICend,$covered_MACstart,$MACend"}){
print "Conflict MIC canonical merging: \nnow: ".$records."\n".${$MICbased_canonical_Merge_record{$MICname}{$MACname}}{"$new_MICstart,$new_MICend,$covered_MACstart,$MACend"}."\n";
}
$MACbased_canonical_Merge_record{$MACname}{$MICname}{"$covered_MACstart,$MACend,$new_MICstart,$new_MICend"}=$records;
$MICbased_canonical_Merge_record{$MICname}{$MACname}{"$new_MICstart,$new_MICend,$covered_MACstart,$MACend"}=$records;
$MAChsp_TMR{$MACname}{$MICname}{"$covered_MACstart.$covered_MACend"}=$records;
$MAChsp_TMR{$MACname}{$MICname}{"$MACstart.$MACend"}=$records;
$canonical_merged_MAC_MIC_combinations{"${MACname}_$MICname"}++;
print Canonical_section ("Merged,$MACname,$MICname,section1,$covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend,$covered_strand,section2,$MACstart,$MACend,$MICstart,$MICend,$strand\n");
Delete_MAC_MIC_pos($MACname,$MICname,"$covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend",\%step02_Tyically_Merged_HSP_List);
Delete_MAC_MIC_pos($MACname,$MICname,"$MACstart,$MACend,$MICstart,$MICend",\%step02_Tyically_Merged_HSP_List);
@inf[3,5,6,7,8,12]=("canonical_merge",$covered_MACstart,$MACend,$new_MICstart,$new_MICend,$new_Strand);
$HSP_infos=join ",",@inf;
($MACstart,$MACend,$MICstart,$MICend,$strand)=($covered_MACstart,$MACend,$new_MICstart,$new_MICend,$new_Strand);
$dealted=1;
last;
}
}
}
goto anchor_2 if($dealted==1);
${$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"}=$HSP_infos if ($dealted==0);
}
# [c2-Complete: canonical merge]
}
}
print " ] DONE !\n";
# [c3-integrate the merged hits to create a MDSlist]
our %step03_MDSlist;
my $process=0;
print " Building MDS list:\t\t[ ";
my $time_begin=time();
my $time_here=0;
for my $MACname( sort { $a cmp $b } keys %step02_Tyically_Merged_HSP_List){
$process++;
print "=" if( $process%((keys %step02_Tyically_Merged_HSP_List)/20)==0);
#for my $strand( sort { $a cmp $b } keys %{$step02_Tyically_Merged_HSP_List{$MACname}}){
my %sortlist;
for my $MICname(sort { $a cmp $b } keys %{$step02_Tyically_Merged_HSP_List{$MACname}}){
for my $info (sort { $a cmp $b } values %{$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}}){
my @inf=split /,/,$info; #qseqid sseqid pident length mismatch qstart qend sstart send evalue bitscore qcovs (strand)
unless(@inf==13){
print "\n [Error][The contents of %step02_Tyically_Merged_HSP_List is incomplete or empty!]\n";
print Error_log ("\n [Error][The contents of %step02_Tyically_Merged_HSP_List is incomplete or empty!]\n");
}
$sortlist{$info}=$inf[5];
}
}
for my $info( sort { $sortlist{$a} <=> $sortlist{$b} } keys %sortlist ){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$bitScore,$strand)=(split /,/,$info)[1,5,6,7,8,10,12];
my $MIClen=$MIClen{$MICname};
anchor_3:
my $dealted=0;
goto add_new if(exists ${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"});
# (c3.1) merge the identical or nearly identical hits. only less than 1 bp is accepted
for my $existed_inf(sort {$step03_MDSlist{$MACname}{$a}<=>$step03_MDSlist{$MACname}{$b}} keys %{$step03_MDSlist{$MACname}}){
my @existed_infos = split /,/,$existed_inf;
next unless(@existed_infos==7);
my ($existed_MICname,$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend,$existed_strand)=@existed_infos[1,2,3,4,5,6];
my $existed_Score=(split /,/,$step01_HSP_list{$MACname}{$existed_MICname}{"$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend"})[-2];
if( abs($MACstart-$existed_MACstart)<=1 and abs($MACend-$existed_MACend)<=1 ){
$dealted=&remove_low_confidence($MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand,$bitScore,$existed_MICname,$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend,$existed_strand,$existed_Score);
last;
}
}
next if($dealted==1);
goto anchor_3 if($dealted==3);
# (c3.2) merge the nested hits after canonically merging
for my $existed_inf(sort {$step03_MDSlist{$MACname}{$a}<=>$step03_MDSlist{$MACname}{$b}} keys %{$step03_MDSlist{$MACname}}){
my @existed_infos = split /,/,$existed_inf;
next unless(@existed_infos==7);
my ($existed_MICname,$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend,$existed_strand)=@existed_infos[1,2,3,4,5,6];
my $existed_Judgement_MACstart=( abs($MACstart-$existed_MACstart)<=1 ) ? $MACstart : $existed_MACstart;
my $existed_Judgement_MACend=( abs($MACend-$existed_MACend)<=1 ) ? $MACend : $existed_MACend;
next unless( ($MACstart<=$existed_Judgement_MACstart and $existed_Judgement_MACend<=$MACend) or ($existed_Judgement_MACstart<=$MACstart and $MACend<=$existed_Judgement_MACend) );
if($MACend-$MACstart > $existed_MACend-$existed_MACstart and
( !exists ${$MACbased_canonical_Merge_record{$MACname}{$existed_MICname}}{"$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend"} or
exists ${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"}
)
){
&Delete_MAC_pos($MACname,$existed_inf,\%step03_MDSlist);
$dealted=3;
}elsif($MACend-$MACstart < $existed_MACend-$existed_MACstart and
(!exists ${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{"$MACstart,$MACend,$MICstart,$MICend"} or
exists ${$MACbased_canonical_Merge_record{$MACname}{$existed_MICname}}{"$existed_MACstart,$existed_MACend,$existed_MICstart,$existed_MICend"}
)
){
&Delete_MAC_pos($MACname,"$MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand",\%step03_MDSlist);
$dealted=1;
}
last;
}
next if($dealted==1);
goto anchor_3 if($dealted==3);
# (c3.3) add a new one
add_new:
$step03_MDSlist{$MACname}{"$MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MACstart.$MACend" if($dealted==0);
}
}
print " ] DONE !\n";
# [c3-Complete: integrate the merged hits to create a MDSlist]
# [c4- split the canonically merged hits]
for my $MACname(sort {$a cmp $b} keys %step03_MDSlist){
my $dealted=0;
for my $MACinfo(sort {$step03_MDSlist{$MACname}{$a} <=> $step03_MDSlist{$MACname}{$b}} keys %{$step03_MDSlist{$MACname}}){
my %contents;
my $MACpos=$step03_MDSlist{$MACname}{$MACinfo};
my ($tmpMACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
my $key_of_canonical_Merge_record="$MACstart,$MACend,$MICstart,$MICend";
if(exists ${$MACbased_canonical_Merge_record{$MACname}{$MICname}}{$key_of_canonical_Merge_record}){
extract_raw_inf_of_Canonically_Merged(\%MACbased_canonical_Merge_record,$MACname,$MICname,$key_of_canonical_Merge_record,\%contents);
Delete_MAC_pos($MACname,$MACinfo,\%step03_MDSlist);
}
for my $pos (sort {$a<=>$b} keys %contents){
my ($MACstart,$MACend,$MICstart,$MICend)=split /,/,$pos;
my $info=$contents{$pos};
$step03_MDSlist{$MACname}{$info}="$MACstart.$MACend";
}
}
}
# [c4-Complete: split the canonical merged hits]
# transport the data that based on MAC_id to a new hash based on MIC_id
our %step05_MIC_MDSlist;
for my $MACname(sort {$a cmp $b} keys %step03_MDSlist){
for my $MACinfo(sort {$step03_MDSlist{$MACname}{$a} <=> $step03_MDSlist{$MACname}{$b}} keys %{$step03_MDSlist{$MACname}}){
my ($tmpMACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
chomp $MICend;
if($MICstart<=0 or $MICend<=0){
print "\nError: line304: $MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand\n"
}
$step05_MIC_MDSlist{$MICname}{"$MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MICstart.$MICend";
}
}
# trim incomplete MDS segments caused by poor assembly quality
our %step06_MIC_MDSlist;
for my $MICname (sort {$a cmp $b} keys %step05_MIC_MDSlist){
#next if($needless_realMICs{$MICname}>0);
for my $MICinfo (sort {$step05_MIC_MDSlist{$MICname}{$a} <=> $step05_MIC_MDSlist{$MICname}{$b}} keys %{$step05_MIC_MDSlist{$MICname}}){
my ($MACname,$MICtmp,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
Check_again_c5_5:
my $keep_the_behind_one=1;
for my $MICinfo_front (sort {$step06_MIC_MDSlist{$MICname}{$a} <=> $step06_MIC_MDSlist{$MICname}{$b}} keys %{$step06_MIC_MDSlist{$MICname}}){
my ($MACname_front,$MICtmp_front,$MACstart_front,$MACend_front,$MICstart_front,$MICend_front,$strand_front)=split /,/,$MICinfo_front;
next if($MAC_tel_5{$MACname}>0 or $MAC_tel_3{$MACname}>0);
my $MAC_len=$MAClen{$MACname};
my $MAC_front_len=$MAClen{$MACname_front};
if( $MICstart_front<$MICstart and $MICend<=$MICend_front and $MACstart<=2 and abs($MACend-$MAC_len)<=1 ){ # keep the front one
$keep_the_behind_one=0;
last
}elsif($MICstart_front==$MICstart and $MICend_front<=$MICend and abs($MACend_front-$MAC_front_len)<=1 ){ # keep the behind one
delete ${$step06_MIC_MDSlist{$MICname}}{$MICinfo_front} if(exists ${$step06_MIC_MDSlist{$MICname}}{$MICinfo_front} );
$keep_the_behind_one=2;
last;
}
}
$step06_MIC_MDSlist{$MICname}{$MICinfo}=$step05_MIC_MDSlist{$MICname}{$MICinfo} if($keep_the_behind_one==1);
goto Check_again_c5_5 if($keep_the_behind_one==2);
}
}
# transport the trimmed data to a MAC_id based hash
our %step07_MDSlist;
for my $MICname(sort {$a cmp $b} keys %step06_MIC_MDSlist){
#next if($needless_realMICs{$MICname}>0);
for my $MICinfo (sort {$step06_MIC_MDSlist{$MICname}{$a} <=> $step06_MIC_MDSlist{$MICname}{$b}} keys %{$step06_MIC_MDSlist{$MICname}}){
my ($MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
$step07_MDSlist{$MACname}{$MICname}{"$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MACstart.$MACend";
}
}
my $process=0;
our %step08_MDSlist;
print " Final Checking :\t\t[ ";
for my $MACname (sort {$a cmp $b} keys %step07_MDSlist){
$process++;
print "=" if( $process%((keys %step07_MDSlist)/20)==0);
# (c6) connect the HSPs which may be splited unexpectedly
for my $MICname (sort {$a cmp $b} keys %{$step07_MDSlist{$MACname}}){
for my $MACinfo (sort {$step07_MDSlist{$MACname}{$MICname}{$a} <=> $step07_MDSlist{$MACname}{$MICname}{$b}} keys %{$step07_MDSlist{$MACname}{$MICname}}){
my ($MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
Check_again_c6:
my $dealted=0;
for my $covered_info (sort {$step08_MDSlist{$MACname}{$a} <=> $step08_MDSlist{$MACname}{$b}} keys %{$step08_MDSlist{$MACname}}){
my ($covered_MICname,$covered_MACstart,$covered_MACend,$covered_MICstart,$covered_MICend,$covered_strand)=split /,/,$covered_info;
next if($covered_strand ne $strand or $covered_MICname ne $MICname ) ;
my $limit_MAC=abs($MACend-$covered_MACstart+1)*$max_overlaps;
my $limit_MIC=abs($MICend-$covered_MICstart+1)*$max_overlaps;
if( $covered_MACstart<=$MACstart and $MACstart<=$covered_MACend and $covered_MACend-$MACstart<=$limit_MAC and $covered_MACend<=$MACend
and $covered_MICstart<=$MICstart and $MICstart<=$covered_MICend and $covered_MICend-$MICstart<=$limit_MIC and $covered_MICend<=$MICend
and !exists ${$MAChsp_TMR{$MACname}{$MICname}}{"$MACstart.$MACend"} and !exists ${$MAChsp_TMR{$MACname}{$MICname}}{"$covered_MACstart.$covered_MACend"}
){
&Delete_MAC_pos($MACname,"$MICname,$MACinfo",\%step08_MDSlist);
&Delete_MAC_pos($MACname,$covered_info,\%step08_MDSlist);
($MACstart,$MACend,$MICstart,$MICend)=($covered_MACstart,$MACend,$covered_MICstart,$MICend);
$dealted=2;
last;
}
}
goto Check_again_c6 if($dealted==2);
$step08_MDSlist{$MACname}{"$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MACstart.$MACend" if($dealted==0);
}
}
}
our %step09_MDSlist;
for my $MACname (sort {$a cmp $b} keys %step08_MDSlist){
# (c7) deprecated. nothing changed
for my $MACinfo (sort {$step08_MDSlist{$MACname}{$a} <=> $step08_MDSlist{$MACname}{$b}} keys %{$step08_MDSlist{$MACname}}){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
my $MIClen=$MIClen{$MICname};
my $MAClen=$MAClen{$MACname};
$step09_MDSlist{$MACname}{"$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MACstart.$MACend";
}
}
# remove the nested MDSs on MAC
for my $MACname (sort {$a cmp $b} keys %step09_MDSlist){
my @infos=sort {$step09_MDSlist{$MACname}{$a} <=> $step09_MDSlist{$MACname}{$b}} keys %{$step09_MDSlist{$MACname}};
my %wait2delete_MACmds;
for my $inf (@infos){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$inf;
for my $inf2 (@infos){
next if(exists $wait2delete_MACmds{$inf2});
my ($existed_MICname,$asRef_MACstart,$asRef_MACend,$asRef_MICstart,$asRef_MICend,$asRef_strand)=split /,/,$inf2;
if($asRef_MACstart<=$MACstart and $MACend<=$asRef_MACend and $step09_MDSlist{$MACname}{$inf2}!=$step09_MDSlist{$MACname}{$inf} and
!(exists ${$MAChsp_TMR{$MACname}{$MICname}}{"$MACstart.$MACend"} and !exists ${$MAChsp_TMR{$MACname}{$existed_MICname}}{"$asRef_MACstart.$asRef_MACend"} )
){
$wait2delete_MACmds{$inf}++;
$inf=~s/,/\t/g;
$inf2=~s/,/\t/g;
my $output_inf="#[hypothetical-Nested]\nmac:$MACname\n";
$output_inf.="mic:$MICname is involved in Canonically-Merging\n" if(exists ${$MAChsp_TMR{$MACname}{$MICname}}{"$MACstart.$MACend"});
$output_inf.="mic:$existed_MICname is involved in Canonically-Merging\n" if(exists ${$MAChsp_TMR{$MACname}{$existed_MICname}}{"$asRef_MACstart.$asRef_MACend"});
$output_inf.="inf1:$inf\ninf2:$inf2\n";
print Error_log $output_inf;
}
}
}
for my $inf (keys %wait2delete_MACmds){ delete ${$step09_MDSlist{$MACname}}{$inf} }
my $dealted=1;
while($dealted==0){
$dealted=0;
my @infos=sort {$step09_MDSlist{$MACname}{$a} <=> $step09_MDSlist{$MACname}{$b}} keys %{$step09_MDSlist{$MACname}};
for(my $i=0;$i<@infos;$i++){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$infos[$i];
for(my $k=$i+2;$k<@infos;$k++){
my ($check_MICname,$check_MACstart,$check_MACend,$check_MICstart,$check_MICend,$check_strand)=split /,/,$infos[$k];
my $insert_MDSs=$infos[($k-1)];
my ($insert_MIC,$insert_MACstart,$insert_MACend)=(split /,/,$insert_MDSs)[0,1,2];
if($check_MACstart<=$MACend and !exists ${$MAChsp_TMR{$MACname}{$insert_MIC}}{"$insert_MACstart.$insert_MACend"}){
my $records="#[hypothetical-Insertion]\nmac:$MACname\nThis MDSs: $insert_MDSs\nis An Insertion Between $infos[$i] \nand $infos[$k]\n";
print Error_log $records;
delete ${$step09_MDSlist{$MACname}}{$infos[($k-1)]} ;
$dealted=1;
last;
}elsif($check_MACstart>$MACend){
last;
}
}
}
}
}
print " ] DONE !\n";
my %final_MIC_MDSlist;
my %Preparation_for_IESidentify;
my %IESsource;
my %MIC_IESs;
#
for my $MACname (sort {$a cmp $b} keys %step09_MDSlist){
for my $MACinfo (sort {$step09_MDSlist{$MACname}{$a} <=> $step09_MDSlist{$MACname}{$b}} keys %{$step09_MDSlist{$MACname}}){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
$final_MIC_MDSlist{$MICname}{"$MACname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MICstart.$MICend";
$Preparation_for_IESidentify{"$MICname,$MACname"}{"$MACname,$MACstart,$MACend,$MICstart,$MICend,$strand"}="$MICstart.$MICend";
}
}
# identify IESs from each MAC-MIC pairs
for my $ctgname (sort keys %Preparation_for_IESidentify){
my ($MICname,$MACname)=split /,/,$ctgname;
my $last_MICstart=0;
my $last_MICend=0;
my $last_MACstart=0;
my $last_MACend=0;
for my $MICinfo (sort {$Preparation_for_IESidentify{$ctgname}{$a} <=> $Preparation_for_IESidentify{$ctgname}{$b}} keys %{$Preparation_for_IESidentify{$ctgname}}){
my ($MACname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
if($last_MICstart>0){
my $IESstart=$last_MICend+1;
my $IESstop=$MICstart-1;
next if($IESstart>$IESstop);
if( $IESstart<=$IESstop and ($last_MACstart<=$MACstart and $MACstart<=$last_MACend and $last_MACend<=$MACend ) or ($MACstart<=$last_MACstart and $last_MACstart<=$MACend and $MACend<=$last_MACend ) ){
$IESsource{$MICname}{"$IESstart.$IESstop"}="Hiconf";
$MIC_IESs{$MICname}{$MICinfo}="$IESstart.$IESstop";
}
}
($last_MICstart,$last_MICend,$last_MACstart,$last_MACend)=($MICstart,$MICend,$MACstart,$MACend);
}
}
# identify IESs according MIC MDSs coordinates
for my $MICname (sort keys %final_MIC_MDSlist){
my $last_MICstart=0;
my $last_MICend=0;
my $last_MACstart=0;
my $last_MACend=0;
my $last_MACname;
for my $MICinfo (sort {$final_MIC_MDSlist{$MICname}{$a} <=> $final_MIC_MDSlist{$MICname}{$b}} keys %{$final_MIC_MDSlist{$MICname}}){
my ($MACname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
if($last_MICstart>0){
my $IESstart=$last_MICend+1;
my $IESstop=$MICstart-1;
if($IESstart<=$IESstop){
$IESsource{$MICname}{"$IESstart.$IESstop"}="Midconf" if($MACname eq $last_MACname and !exists $IESsource{$MICname}{"$IESstart.$IESstop"});
$MIC_IESs{$MICname}{$MICinfo}="$IESstart.$IESstop" if(!exists $IESsource{$MICname}{"$IESstart.$IESstop"});
}
}
($last_MACname,$last_MICstart,$last_MICend,$last_MACstart,$last_MACend)=($MACname,$MICstart,$MICend,$MACstart,$MACend);
}
}
# =============================================================================================================================================================================================== #
# Output Results #
# =============================================================================================================================================================================================== #
# Output Final Results
print " Output Final result:\t\t[ ";
my $total_outFiles=9;
my $part=int(20/$total_outFiles);
my $last_part=20-$part*($total_outFiles-1);
# file1
outPut_MDSlist_style1("$outPath/Progess/middle.step03_MDSlist","tsv",\%step03_MDSlist,1);
print "=" for(1..$part);
# file2
outPut_MDSlist_style2("$outPath/Progess/middle.step07_MDSlist","tsv",\%step07_MDSlist,2);
print "=" for(1..$part);
# file3
outPut_MDSlist_style1("$outPath/Progess/middle.step08_MDSlist","tsv",\%step08_MDSlist,3);
print "=" for(1..$part);
# file4
outPut_MDSlist_style1("$outPath/Progess/middle.step09_MDSlist","tsv",\%step09_MDSlist,3);
my $mac_out_base="$outPath/MAC.annotation/mac.mds.structures";
open MACannotationTAB,">","$mac_out_base.tab" or die "Fail to open mac.mds.structures.tab!\n";
open MACannotationCSV,">","$mac_out_base.csv" or die "Fail to open mac.mds.structures.csv!\n";
open MACannotationGFF,">","$mac_out_base.gff3" or die "Fail to open mac.mds.structures.gff3!\n";
my $head_inf="MACname,MICname,type,MACstart,MACstop,MICstart,MICstop,strand\n";
print MACannotationCSV $head_inf;
$head_inf=~s/,/\t/g;
print MACannotationTAB $head_inf;
$head_inf="#gff-version3\n";
print MACannotationGFF $head_inf;
for my $MACname(sort {$a cmp $b} keys %step09_MDSlist){
#my $MAClen=$MAClen{$MACname};
my $circle_time=1;
my $MACscaff_code=$MAC_scaff_codes{$MACname};
my $Tel5_len=$MAC_tel_5{$MACname};
my $Tel3_len=$MAC_tel_3{$MACname};
my $MAClen=$MAClen{$MACname}+$Tel5_len+$Tel3_len;
my $tel3_start=$MAClen-$Tel3_len;
print MACannotationGFF "##sequence-region 1 $MAClen\n";
if ($Tel5_len>0){
my $outinf="$MACname,NA,telo5p,1,$Tel5_len,0,0,+\n";
print MACannotationCSV $outinf;
$outinf=~s/,/\t/g;
print MACannotationTAB $outinf;
#$outinf=&GFFformat($MACname,"Perl","telomere","1",$Tel5_len,".","+",".","telo5p.$MACscaff_code","");
#print MACannotationGFF $outinf;
}
my $tel5_start=$Tel5_len+1 if($Tel5_len>0);
my $out_CSV;
my $out_GFF;
for my $MACinfo(sort {$step09_MDSlist{$MACname}{$a} <=> $step09_MDSlist{$MACname}{$b}} keys %{$step09_MDSlist{$MACname}}){
my ($MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MACinfo;
$MACstart+=$Tel5_len;
$MACend+=$Tel5_len;
my $OUT_start;
my $OUT_stop;
if($Tel5_len>0 and $MACstart<$Tel5_len and $Tel3_len>0 and $MACend>$tel3_start){
$OUT_start=$tel5_start;
$OUT_stop=$tel3_start;
}elsif($Tel5_len>0 and $MACstart<$Tel5_len){
$OUT_start=$tel5_start;
$OUT_stop=$MACend;
}elsif($Tel3_len>0 and $MACend>$tel3_start){
$OUT_start=$MACstart;
$OUT_stop=$tel3_start;
}else{
$OUT_start=$MACstart;
$OUT_stop=$MACend;
}
my $out_v4csv.="$MACname,mds_$circle_time,$strand,$OUT_start,$OUT_stop\n";
$out_CSV.="$MACname,$MICname,mds_$circle_time,$OUT_start,$OUT_stop,$MICstart,$MICend,$strand,mds.$MACscaff_code.$circle_time\n";
$out_GFF.=&GFFformat($MACname,"Perl","mds",$OUT_start,$OUT_stop,".","$strand",".","mds.$MACscaff_code.$circle_time","Target=$MICname ${MICstart} $MICend $strand;");
$circle_time++;
}
print MACannotationCSV $out_CSV;
$out_CSV=~s/,/\t/g;
print MACannotationTAB $out_CSV;
print MACannotationGFF $out_GFF;
$tel3_start++;
if ($Tel3_len>0){
my $outinf="$MACname,NA,telo3p,$tel3_start,$MAClen,0,0,+\n";
print MACannotationCSV $outinf;
$outinf=~s/,/\t/g;
print MACannotationTAB $outinf;
#$outinf=&GFFformat($MACname,"Perl","telomere",$tel3_start,$MAClen,".","+",".","telo3p.$MACscaff_code","");
#print MACannotationGFF $outinf;
}
}
close MACannotationGFF;
close MACannotationCSV;
close MACannotationTAB;
print "=" for(1..$part);
open HSP_lists,">","$outPath/Progess/middle.step01_HSP_list.tsv" or die $!;
for my $MACname( sort { $a cmp $b } keys %step01_HSP_list){
for my $MICname( sort { $a cmp $b } keys %{$step01_HSP_list{$MACname}}){
for my $coordinate (sort by_MAC_hsp_coordinate keys %{$step01_HSP_list{$MACname}{$MICname}}){
my $HSP_infos=$step01_HSP_list{$MACname}{$MICname}{$coordinate};
$HSP_infos=~s/,/\t/g;
print HSP_lists $HSP_infos."\n";
}
}
}
print "=" for(1..$part);
open Tyically_Merged_HSP_List_MACbased,">","$outPath/Progess/middle.step02_Tyically_Merged_HSP_List.MACbased.tsv" or die $!;
for my $MACname( sort { $a cmp $b } keys %MACbased_canonical_Merge_record){
for my $MICname( sort { $a cmp $b } keys %{$MACbased_canonical_Merge_record{$MACname}}){
for my $coordinate (sort by_MAC_hsp_coordinate keys %{$MACbased_canonical_Merge_record{$MACname}{$MICname}}){
my $HSP_infos=$MACbased_canonical_Merge_record{$MACname}{$MICname}{$coordinate};
$HSP_infos=~s/,/\t/g;
print Tyically_Merged_HSP_List_MACbased $HSP_infos."\n";
}
}
}
open Tyically_merged_HSP_list,">","$outPath/Progess/middle.step02_Tyically_Merged_HSP_List.tsv" or die $!;
for my $MACname( sort { $a cmp $b } keys %step02_Tyically_Merged_HSP_List){
for my $MICname( sort { $a cmp $b } keys %{$step02_Tyically_Merged_HSP_List{$MACname}}){
for my $coordinate (sort by_MAC_hsp_coordinate keys %{$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}}){
my $HSP_infos=$step02_Tyically_Merged_HSP_List{$MACname}{$MICname}{$coordinate};
$HSP_infos=~s/,/\t/g;
print Tyically_merged_HSP_list $HSP_infos."\n";
}
}
}
print "=" for(1..$part);
open step05_MIC_MDSlist,">","$outPath/Progess/middle.step05_MIC_MDSlist" or die $!;
print step05_MIC_MDSlist "#IESs in this file are preliminary predictions and may not be accurate\nMACname,type,strand,start,end\n";
#my ($MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$step05_MIC_MDSlist{$MICname}{$MICpos};
for my $MICname(sort { $a cmp $b } keys %step05_MIC_MDSlist){
my $MIClen=$MIClen{$MICname};
my $last_MICend=0;
my $mds_order=1;
my $ies_order=1;
my $last_MACname;
for my $MICinfo (sort {$step05_MIC_MDSlist{$MICname}{$a} <=> $step05_MIC_MDSlist{$MICname}{$b}} keys %{$step05_MIC_MDSlist{$MICname}}){
my ($MACname,$MICname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
if($last_MICend>0 and $last_MICend<$MICstart ){
my $attribude=( $last_MACname eq $MACname ) ? "Hiconf" : "Pred" ; # Hic refers to High-Confidence, Prd refers to Predicited
my $ies_start=$last_MICend+1;
my $ies_stop=$MICstart-1;
print step05_MIC_MDSlist "$MICname,${attribude}ies$ies_order,$strand,$ies_start,$ies_stop\n";
$ies_order++;
}
print step05_MIC_MDSlist "$MICname,mds$mds_order,$strand,$MICstart,$MICend\n";
$mds_order++;
$last_MICend=$MICend;
$last_MACname=$MACname;
}
}
print "=" for(1..$part);
# MICname final_MIC_MDSlist
open MIC_MDSlist,">","$outPath/Progess/middle.final_MIC_MDSlist.tsv" or die $!;
my $out_base="$outPath/MIC.annotation/mic.mds.structures";
open MICannotationTAB,">","$out_base.tab" or die $!;
open MICannotationGFF,">","$out_base.gff3" or die $!;
open MICannotationCSV,">","$out_base.csv" or die $!;
my $out="MICname,type,strand,start,end\n";
$out=~s/,/\t/g;
print MIC_MDSlist $out;
$out="MACname\tMICname\ttype\tMACstart\tMACstop\tMICstart\tMICstop\tstrand\n";
print MICannotationTAB $out;
$out=~s/\t/,/g;
print MICannotationCSV $out;
print MICannotationGFF "#gff-version3\n";
for my $MICname(sort { $a cmp $b } keys %final_MIC_MDSlist){
my $MIClen=$MIClen{$MICname};
my $mds_order=1;
my $ies_order=1;
my $MICscaff_code=$MIC_scaff_codes{$MICname};
#my $head=&GFFformat($MICname,"Perl","supercontig","1",$MIClen,".","+",".","mic.$MICscaff_code","");
print MICannotationGFF "##sequence-region 1 $MIClen\n";
for my $MICinfo(sort {$final_MIC_MDSlist{$MICname}{$a} <=> $final_MIC_MDSlist{$MICname}{$b}} keys %{$final_MIC_MDSlist{$MICname}}){
my ($MACname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
my $MACtelo5_len=$MAC_tel_5{$MACname};
$MACstart+=$MACtelo5_len;
$MACend+=$MACtelo5_len;
my $out="$MICname,mds$mds_order,$strand,$MICstart,$MICend\n";
$out=~s/,/\t/g;
print MIC_MDSlist $out;
$out="$MACname\t$MICname\tmds$mds_order\t$MACstart\t$MACend\t$MICstart\t$MICend\t$strand\tmds.$MICscaff_code.$mds_order\n";
print MICannotationTAB $out;
$out=~s/\t/,/g;
print MICannotationCSV $out;
my $out_GFF=&GFFformat($MICname,"Perl","mds",$MICstart,$MICend,".","$strand",".","mds.$MICscaff_code.$mds_order","Target=$MACname ${MACstart} $MACend $strand;Note=NA;");
print MICannotationGFF "$out_GFF";
$mds_order++;
}
my $last_MACname="";
for my $MICinfo(sort {$MIC_IESs{$MICname}{$a} <=> $MIC_IESs{$MICname}{$b}} keys %{$MIC_IESs{$MICname}}){
my ($MACname,$MACstart,$MACend,$MICstart,$MICend,$strand)=split /,/,$MICinfo;
my $MICpos=$MIC_IESs{$MICname}{$MICinfo};
my ($IESstart,$IESend)=split /\./,$MICpos;
my $attribude= (exists ${$IESsource{$MICname}}{$MICpos}) ? $IESsource{$MICname}{$MICpos} : "Pred" ;
my $out="$MICname,ies$ies_order,$strand,$MICstart,$MICend\n";
$out=~s/,/\t/g;
print MIC_MDSlist $out;
$out="NA\t$MICname\t${attribude}ies$ies_order\tNA\tNA\t$IESstart\t$IESend\tNA\ties.$MICscaff_code.$ies_order";
print MICannotationTAB "$out\n";
$out=~s/\t/,/g;
print MICannotationCSV "$out\n";
my $out_GFF=&GFFformat($MICname,"Perl","ies",$IESstart,$IESend,".","$strand",".","ies.$MICscaff_code.$ies_order","Target=$MACname . . .;Note=$attribude;");
print MICannotationGFF "$out_GFF";
$ies_order++;
$last_MACname=$MACname;
}
}
close MICannotationCSV;
close MICannotationTAB;
close MICannotationGFF;
print "=" for(1..$part);
# Get the infomation of MIC-algnments
open MICdetails,">","$outPath/Progess/middle.MICbased_elim1st_Blast_result.tsv" or die $!;
for my $MICname(sort {$a cmp $b} keys %MICbased_elim1st_Blast_result){
for my $MICinfo(sort {$MICbased_elim1st_Blast_result{$MICname}{$a}<=>$MICbased_elim1st_Blast_result{$MICname}{$b}} keys %{$MICbased_elim1st_Blast_result{$MICname}}){
$MICinfo=~s/,/\t/g;
print MICdetails "$MICinfo\n";
}
}
close MICdetails;
print "=" for(1..$last_part);
print " ] DONE !\n";
my $time_end=time();
my $timespending=$time_end-$time_start; #sprintf ("%.1f",($time_end-$time_start)/60);
print " All steps cost $timespending s \n";
sub GFFformat {
my ($MACname,$source,$type,$start,$end,$score,$strand,$phase,$attribude_ID,$otherINF)=@_;
my $GFF_format="$MACname\t$source\t$type\t$start\t$end\t$score\t$strand\t$phase\tID=$attribude_ID;$otherINF\n";
return $GFF_format;
}
sub get_reverse_complementry_seq {
my $Seq=shift;
$Seq=tr/ATCG/TAGC/;
$Seq=reverse $Seq;
return $Seq;
}
sub min {
my $Min = shift;
for (@_) {
$Min = $_ if $_ < $Min;
}
return $Min;
}
sub max {
my $Max = shift;
for (@_) {
$Max = $_ if $_ > $Max;
}
return $Max;
}
sub average{
my $aver=0;
my $count=0;
my $total;
while(my $aver=shift){
$total+=$aver;
$count++;
}
$aver=$total/$count;
$aver=sprintf ("%.1f",$aver)
}
sub Delete_MAC_pos {
my $MAC=shift;
my $position=shift;
my $hash=shift;
delete ${$$hash{$MAC}}{$position} if ( defined ${$$hash{$MAC}}{$position} or exists ${$$hash{$MAC}}{$position} );
delete $$hash{$MAC} if (keys %{$$hash{$MAC}}<1);
}
sub Delete_MAC_MIC_pos {
my $MAC=shift;
my $MIC=shift;
my $position=shift;
my $hash=shift;
delete ${$$hash{$MAC}{$MIC}}{$position} if ( defined ${$$hash{$MAC}{$MIC}}{$position} or exists ${$$hash{$MAC}{$MIC}}{$position} );
delete ${$$hash{$MAC}}{$MIC} if (keys %{$$hash{$MAC}{$MIC}}<1);
}
sub sections_separate_or_not {
my ($MICname,$MACname,$section1_MICstart,$section1_MICend,$section1_MACstart,$section1_MACend,$section2_MICstart,$section2_MICend,$section2_MACstart,$section2_MACend,$MACorMIC_based_canonical_Merge_record)=@_;
my %contents1;
my %contents2;
my $key_of_canonical_Merge_record1="$section1_MICstart,$section1_MICend,$section1_MACstart,$section1_MACend";
my $key_of_canonical_Merge_record2="$section2_MICstart,$section2_MICend,$section2_MACstart,$section2_MACend";
extract_raw_inf_of_Canonically_Merged(\%$MACorMIC_based_canonical_Merge_record,$MICname,$MACname,$key_of_canonical_Merge_record1,\%contents1) if(exists ${$$MACorMIC_based_canonical_Merge_record{$MICname}{$MACname}}{$key_of_canonical_Merge_record1});
extract_raw_inf_of_Canonically_Merged(\%$MACorMIC_based_canonical_Merge_record,$MICname,$MACname,$key_of_canonical_Merge_record2,\%contents2) if(exists ${$$MACorMIC_based_canonical_Merge_record{$MICname}{$MACname}}{$key_of_canonical_Merge_record2});
my @querying_Positions;
if((keys %contents1)>0){
for my $pos (sort {$a<=>$b} keys %contents1){
my $qPos="$3.$4" if($pos=~/^(\d+),(\d+),(\d+),(\d+)$/);
push @querying_Positions,$qPos;
}
}else{
push @querying_Positions,"$section1_MICstart.$section1_MICend"
}
if((keys %contents2)>0){
for my $pos (sort {$a<=>$b} keys %contents2){
my $qPos="$3.$4" if($pos=~/^(\d+),(\d+),(\d+),(\d+)$/);
push @querying_Positions,$qPos;
}
}else{
push @querying_Positions,"$section2_MICend.$section2_MICend"
}
my $result='Y';
for(my $i=1;$i<@querying_Positions;$i++){
my $Previous_start=min(split /\./,$querying_Positions[$i-1]);
my $Previous_stop=max(split /\./,$querying_Positions[$i-1]);
my $Behind_start=min(split /\./,$querying_Positions[$i]);
my $Behind_stop=max(split /\./,$querying_Positions[$i]);
if( $Previous_start>=$Behind_stop or $Behind_start>=$Previous_stop ){
}else{
$result='N';last;
}
}
return $result;
}
sub extract_raw_inf_of_Canonically_Merged {
my $canonically_merged_record=shift;
my $MACorMIC_name=shift;
my $corespond_MICorMAC_name=shift;
my $Pos_4containers=shift;
my $result=shift;
my $info=$$canonically_merged_record{$MACorMIC_name}{$corespond_MICorMAC_name}{$Pos_4containers};
unless($info=~/^(.*?),(.*?),s1,(.*?),(.*?),(.*?),(.*?),(.*?),s2,(.*?),(.*?),(.*?),(.*?),(.*)$/){
my $error_inf="\n[Error] Empty Merge_record! MACname(MICname):$MACorMIC_name\tMICname(MACname):$corespond_MICorMAC_name\tposition:$Pos_4containers\n";
print $error_inf;
print Error_log $error_inf;
}
$$result{"$3,$4,$5,$6"}="$1,$2,$3,$4,$5,$6,$7";
$$result{"$8,$9,$10,$11"}="$1,$2,$8,$9,$10,$11,$12";
my $dealted=1;
while($dealted==1){
$dealted=0;
for my $Check_pos_4containers (sort {$a cmp $b} keys %{$result}){
my $info=$$canonically_merged_record{$MACorMIC_name}{$corespond_MICorMAC_name}{$Check_pos_4containers};
if($info=~/^(.*?),(.*?),s1,(.*?),(.*?),(.*?),(.*?),(.*?),s2,(.*?),(.*?),(.*?),(.*?),(.*)$/){
delete $$result{$Check_pos_4containers};
$$result{"$3,$4,$5,$6"}="$1,$2,$3,$4,$5,$6,$7";
$$result{"$8,$9,$10,$11"}="$1,$2,$8,$9,$10,$11,$12";
$dealted++
}
}
}
}
sub get_NewStartAndEnd {
my $section1_start=shift;
my $section1_end=shift;
my $section1_strand=shift;
my $section2_start=shift;
my $section2_end=shift;
my $section2_strand=shift;
my $MACname=shift;
my $MICname=shift;
my @NewStartAndEnd;
$NewStartAndEnd[0]=&min($section1_start,$section1_end,$section2_start,$section2_end);
$NewStartAndEnd[1]=&max($section1_start,$section1_end,$section2_start,$section2_end);
my $new_strand="";
if( $section1_strand eq '-' and $section2_strand eq '-' ){
$new_strand='-'
}
elsif( $section1_strand eq '+' and $section2_strand eq '+'){
$new_strand='+'
}
elsif( $section1_strand ne $section2_strand ){
if($direction_of_MIC{$MACname}{$MICname}{"+"}>$direction_of_MIC{$MACname}{$MICname}{"-"}){
$new_strand='+'
}
else{
$new_strand='-'
}
}
else{
my $error_inf= "[Error][sub get_NewStartAndEnd: the position of two sections are probably wrong!][Some details for debugging: $section1_start,$section1_end\t|\t$section2_start,$section2_end]\n";
print $error_inf;
print Error_log $error_inf;
}
$NewStartAndEnd[2]=$new_strand;
return @NewStartAndEnd;
}
sub by_MAC_hsp_coordinate {
# format of input: "start1,end1,start2,end2"
my @a_site=split /,/,$a;
my @b_site=split /,/,$b;
my $a_pos1="$a_site[0].$a_site[1]";
my $b_pos1="$b_site[0].$b_site[1]";
my $a_pos2="$a_site[2].$a_site[3]";
my $b_pos2="$b_site[2].$b_site[3]";
if($a_pos1 < $b_pos1){
return -1
}elsif($a_pos1 > $b_pos1){
return 1
}elsif( $a_pos2 < $b_pos2){
return -1
}elsif( $a_pos2 > $b_pos2){
return 1
}else{
return -1
}
}
sub by_HSPs_order {
$a=~/(.*?),(.*?),(.*?,.*?,.*?),(.*?),(.*?),(.*?),(.*?),(.*?,.*?,.*)$/;
my ($MACstart_a,$MACend_a,$MICstart_a,$MICend_a)=($4,$5,$6,$7);
my $MIClen_a=$MIClen{$2};
$b=~/(.*?),(.*?),(.*?,.*?,.*?),(.*?),(.*?),(.*?),(.*?),(.*?,.*?,.*)$/;
my ($MACstart_b,$MACend_b,$MICstart_b,$MICend_b)=($4,$5,$6,$7);
my $MIClen_b=$MIClen{$2};
#print "a is $a\tb is $b\n";
if($MACstart_a+1<$MACstart_b){
-1
}
elsif($MACstart_a>1+$MACstart_b){
1
}
elsif($MACend_a<$MACend_b){
-1
}
elsif($MACend_a>$MACend_b){
1
}
elsif($MACstart_a<$MACstart_b){
-1
}
elsif($MACstart_a>$MACstart_b){
1
}
}
sub by_len {
((length $MAChash{$a}) < (length $MAChash{$b})) ? return 1 : return -1
}
sub load_genome {
my $MAC_file=shift;
my $MIC_file=shift;
local $|=1;
print "\n Build a hash for MAC and MIC\t[ ";
load_fasta($MAC_file,\%MAChash,\%MAClen);
my $not_standard=0;
for my $MACname (keys %MAChash){
unless($MACname=~/NODE_(\d+)_/){
$not_standard++;
last;
}
}
if($not_standard==0){
for my $MACname (keys %MAChash){
$MACname=~/NODE_(\d+)_/;
$MAC_scaff_codes{$MACname}=$1;
}
}else{
my $scaff_code=1;
for my $MACname (sort by_len keys %MAChash){
$MAC_scaff_codes{$MACname}=$scaff_code;
$scaff_code++;
}
}
print "==========";
load_fasta($MIC_file,\%MIChash,\%MIClen);
my $not_standard=0;
for my $MICname (keys %MIChash){
unless($MICname=~/NODE_(\d+)_/){
$not_standard++;
last;
}
}
if($not_standard==0){
for my $MICname (keys %MIChash){
$MICname=~/NODE_(\d+)_/;
$MIC_scaff_codes{$MICname}=$1;
}
}else{