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EAHelitronMFE_P
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#!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2023
# Easy to Annotate Helitrons command line, Multi-Threading version (EAHelitron_P) v1.6000 2023/10/05
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
#use LWP::Simple;
use Parallel::ForkManager;
our $MAX_processes=1;
use re 'eval';
sub getLoggingTime {
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
# my $nice_timestamp = sprintf ( "%04d%02d%02d %02d:%02d:%02d",
# $year+1900,$mon+1,$mday,$hour,$min,$sec);
my $nice_timestamp = sprintf ( "%04d%02d%02d_%02d_%02d_%02d",
$year+1900,$mon+1,$mday,$hour,$min,$sec);
return $nice_timestamp;
}
our $timestamp = getLoggingTime();
# print "$timestamp\n";
our $opfn="";
my $verbose;
our $upstreml=3000;
our $downstreml=500;
our $fuzzylv=0;
our $finalCTAGT="ctagt";
our $MFET= -5;
#our $hairpinpattern="[gc]{4}[at]{1}[gc]{1}|[gc]{3}[at]{1}[gc]{2}|[gc]{2}[at]{1}[gc]{3}|[gc]{1}[at]{1}[gc]{4}|[gc]{5}";
our $hairpinpattern="[gc]{4}[at]{1}[gc]{1}|[gc]{3}[at]{1}[gc]{2}|[gc]{2}[at]{1}[gc]{3}|[gc]{1}[at]{1}[gc]{4}|[gc]{5}|[gc]{4}[at]{2}[gc]{1}|[gc]{3}[at]{2}[gc]{2}|[gc]{2}[at]{2}[gc]{3}|[gc]{1}[at]{2}[gc]{4}|[gc]{1}[at]{1}[gc]{1}[at]{1}[gc]{3}|[gc]{1}[at]{1}[gc]{2}[at]{1}[gc]{2}|[gc]{1}[at]{1}[gc]{3}[at]{1}[gc]{1}|[gc]{2}[at]{1}[gc]{1}[at]{1}[gc]{2}|[gc]{2}[at]{1}[gc]{2}[at]{1}[gc]{1}|[gc]{3}[at]{1}[gc]{1}[at]{1}[gc]{1}";
our $TCpattern="TC(TCTACTA|T.TACTA.T|T.TACTAC|.{2}TACTACT|T.TAC.ACT|T.TA.TACT|T.TACT.CT|T.T.CTACT|.CTACTA.T|.{9}TATTAAG)";
our @CTAGT=qw/
CTAGT
CT[AG]GT
CTA[AG]T
CT[AG]{2}T
CT[AG]{2}.{1}
CTAG.{1}
/;
#our $seqfilename ='';
#GetOptions("i=s"=>\$seqfilename,"o=s" => \$opfn,"verbose"=>\$verbose)
#or die("Error in command line arguments\n perl Searchhelitron -o <outputfile> (inputfile)\n");
GetOptions("o=s" => \$opfn,"verbose"=>\$verbose,"u=i"=>\$upstreml,"p=i"=>\$MAX_processes,"d=i"=>\$downstreml,"r=i"=>\$fuzzylv, "T=s" => \$TCpattern,"H=s" => \$hairpinpattern,"E=f" => \$MFET)
or die("[-]Error in command line arguments
Usage: perl EAHelitronMFE_P [options] <input FASTA file>
options:
[-o string|output prefix Default: EAHeli_out]
[-u int|upstream length Default: 3000]
[-d int|downstream length Default: 500]
[-p int |threads number Default: 1]
Advanced options:
[-T string|TC pattern. User's 5'TC pattern]
[-H string|Hairpin pattern. User's Hairpin left pattern]
[-E float|minimum free energy (MFE) threshold, default: -5]
[-r int[0-5]|CTRRt 3' terminal fuzzy level;
0: CTAGT
1: CT[AG]GT
2: CTA[AG]T
3: CT[AG]{2}T
4: CT[AG]{2}.{1}
5: CTAG.{1}
Default: 0]
Note: Easy to Annotate Helitrons command line, include MFE filter and Multi-Threading version (EAHelitronMFE_P) v1.6000 2023/10/05.\n");
if ($fuzzylv>5 or $fuzzylv<0) {
die ("Please input fuzzy levle in int 0 to 5.\n");
}
#say $fuzzylv;
$finalCTAGT = $CTAGT[$fuzzylv];
print "CTAGT fuzzy level: $fuzzylv $finalCTAGT\n";
print "TCpattern: $TCpattern\n";
print "hairpin left sequence pattern: $hairpinpattern\n";
print "upstream length: $upstreml\n";
print "downstream length: $downstreml \n";
print "minimum free energy (MFE): $MFET\n";
# print "CTAGT fuzzy level: $fuzzylv $finalCTAGT\n";
if ($opfn eq ""){
$opfn="EAHeli_out";
print "output prefix:$opfn\n";
}else{
print "output prefix:$opfn\n";
}
###################sub TRseq##########
sub TRseq($)
{
my ($pinseq) = @_;
#say $pinseq;
my $pinseqtr = reverse $pinseq;
#say $pinseqtr;
$pinseqtr =~ tr/ACGTacgt/TGCAtgca/;
#say $pinseqtr;
return $pinseqtr;
}
##################TRseq End#############
our $loadingstarttime=time();
#defined our $seqfilename =<>;
#say "File: $seqfilename";
#while(defined ($seqfilename = <>)){
#chomp ($seqfilename);
#say "That's $seqfilename is going to analysis. ";
#}
#open (SEQFILENAME,$_);
say "Start loading genomeic sequence.";
#if(!open SEQFILENAME,"< $seqfilename"){
# die "File not Found\n";
#}
#if(!open SEQFILENAME,"< $_"){
# die "File not Found\n";
#}
our $Chri=0;
our @Chrname=();
our @Chrseq=();
#@ARGV = qw#'' Not_Find_a_File#;
#say @ARGV;
#say $0;
while(defined(our $seq = <>)){
#while(our $seq = <SEQFILENAME>){
if ($seq =~ m/^.*>/) {
#$seq=~ m/^.*>(\w+) ?.*/;
#$seq=~ m/^.*>([a-zA-Z0-9_.-]+) ?.*/;
$seq=~ m/^\s*>\s*(\S+)\s*(.*)/; #1.52 new RE based on BioPerl
say $1;
$Chrname[$Chri]= $1;
$Chri++;
}else{
$seq =~ s/\s//;
$seq =~ tr/MRWSYKVHDBmrwsykvhdb/CGTGCGGCGGCGTGCGGCGG/;#1.31add snp replace
$Chrseq[$Chri-1] .=$seq;
}
}
#close SEQFILENAME;
our $loadingendtime=time();
say "$Chri Sequences";
if ($MAX_processes>$Chri){
$MAX_processes=$Chri;
}
print "Finished loading! ";
printf "%g Sec %g Min\n",$loadingendtime-$loadingstarttime,($loadingendtime-$loadingstarttime)/60;
print "Using $MAX_processes thread(s).\n";
our $starttime=time();
#our $hairpinpattern="cccgccc";
#say our $testseq='([atcg]{10}([gc]{4}[at]{1}[gc]{1}|[gc]{3}[at]{1}[gc]{2}|[gc]{2}[at]{1}[gc]{3}|[gc]{1}[at]{1}[gc]{4}|[gc]{5})([atcg]{0,4}[at]{1}[atgc]{0,4})(??{TRseq($2)})([atcg]{3,12}ctagt)[atcgn]{4})';
#say our $testseq='([atcg]{10}([gc]{4}[at]{1}[gc]{1}|[gc]{3}[at]{1}[gc]{2}|[gc]{2}[at]{1}[gc]{3}|[gc]{1}[at]{1}[gc]{4}|[gc]{5})([atcg]{0,4}[at]{1}[atgc]{0,4})(??{TRseq($2)})([atcg]{3,12}'."$finalCTAGT".')[atcgn]{4})';
say our $testseq='([atcg]{10}('."$hairpinpattern".')([atcg]{0,4}[at]{1}[atgc]{0,4})(??{TRseq($2)})([atcg]{3,12}'."$finalCTAGT".')[atcgn]{4})';
#say our $TCseq='([atgcn]{5}(TC(TCTACTA|T.TACTA.T|T.TACTAC|.{2}TACTACT|T.TAC.ACT|T.TA.TACT|T.TACT.CT|T.T.CTACT|.CTACTA.T|.{9}TATTAAG))[atgcn]{20})';
say our $TCseq='([atgcn]{5}('."$TCpattern".')[atgcn]{20})';
say "Running. Please wait for a few minutes.";
#####################################
#Start main
#####################################
# open RSUT,">>$opfn.3.txt";
# open FASTARESULT,">>$opfn.u$upstreml.fa";
# open TCRSUT, ">>$opfn.5.txt";
# open TCFARESULT, ">>$opfn.5.fa";
# open OUTGFF, ">>$opfn.gff3";
# print OUTGFF "##gff-version 3\n";
# open DOWNFA,">> $opfn.down$downstreml.fa" or die ("[-] Error: Can't open or create $opfn.down$downstreml.fa\n");
open RSUT,"> $opfn.3.txt" or die ("[-] Error: Can't open or create $opfn.3.txt\n");
open FASTARESULT,"> $opfn.u$upstreml.fa" or die ("[-] Error: Can't open or create $opfn.u$upstreml.fa\n");
open TCRSUT, "> $opfn.5.txt" or die ("[-] Error: Can't open or create $opfn.5.txt\n");
open TCFARESULT, "> $opfn.5.fa" or die ("[-] Error: Can't open or create $opfn.5.fa\n");
open OUTGFF, "> $opfn.gff3" or die ("[-] Error: Can't open or create $opfn.gff3\n");
print OUTGFF "##gff-version 3\n";
open DOWNFA,"> $opfn.down$downstreml.fa" or die ("[-] Error: Can't open or create $opfn.down$downstreml.fa\n");
open GENOMELENH,"> $opfn.len.txt" or die ("[-] Error: Can't open or create $opfn.len.txt\n");
print GENOMELENH "Seqname\tSeqLength\t[+]\t[-]\tall\t[+]Helitron Density\t[-]Helitron Density\tSeq Helitron Density\n";
open OUTBED, "> $opfn.bed" or die ("[-] Error: Can't open or create $opfn.bed\n");
our $genomel =0;
our $countall=0;
our $count1all=0;
our $count2all=0;
our @count1=();
our @count2=();
our @count1TMP=();
our @count2TMP=();
our $pm=Parallel::ForkManager->new($MAX_processes);
for (our $ni=0;$ni<$Chri;$ni++){
$pm->start and next;
# open RSUTCA,">>cache.$Chrname[$ni].3.txt";
# open FASTARESULTCA,">>cache.$Chrname[$ni].u$upstreml.fa";
# open TCRSUTCA, ">>cache.$Chrname[$ni].5.txt";
# open TCFARESULTCA, ">>cache.$Chrname[$ni].5.fa";
# open OUTGFFCA, ">>cache.$Chrname[$ni].gff3";
# open DOWNFACA, ">>cache.$Chrname[$ni].down$downstreml.fa";
open RSUTCA,">cache.$Chrname[$ni].3.txt";
open FASTARESULTCA,">cache.$Chrname[$ni].u$upstreml.fa";
open TCRSUTCA, ">cache.$Chrname[$ni].5.txt";
open TCFARESULTCA, ">cache.$Chrname[$ni].5.fa";
open OUTGFFCA, ">cache.$Chrname[$ni].gff3";
open DOWNFACA, ">cache.$Chrname[$ni].down$downstreml.fa";
open OUTBEDCA, ">cache.$Chrname[$ni].bed";
open GENOMELENHCA, ">cache.$Chrname[$ni].len.txt";
say "Deal with $Chrname[$ni].";
$count1=1;
$count1[$ni]=1;
$count1TMP[$ni]=0;
our $seqall = $Chrseq[$ni];
################Start deal with plus seqs.################
while ($seqall=~ /$testseq/igc){
#while ($seqall =~ /$testseq/igc){
#say $seqfilename;
#say "Chrom:",$AN;
# $count1++;
# $count1[$ni]++; ## 2023.10.05 move to the last step.
$count1TMP[$ni]++;
our $l3=length ($3);
our $l1=length ($1);
our $seqpos=pos($seqall)-5;
our $seqstarpos=$seqpos-$l1+16;
our $seqdownpos=$seqpos+$downstreml;
our $ChrID=$Chrname[$ni];
our $HID ="$ChrID"."H$count1";
##### Calculate MFE
#say $HID;
my $tmp_hairpin_name = "cache.$timestamp.$opfn.$HID.tmp.".$count1TMP[$ni];
my $tmp_hairpin_fa = substr($1, 0, -9); # Clip last 9 nt.
open TEMPHP,">$tmp_hairpin_name.txt" or die ("[-] Error: Can't open or create temp file $tmp_hairpin_name.txt\n");
print TEMPHP ">tmp.$HID $ChrID:$seqstarpos..$seqpos $l3 $2 $3 $4\n";
print TEMPHP "$tmp_hairpin_fa\n";
close TEMPHP;
## RNAfold
system("RNAfold", "--noPS", "$tmp_hairpin_name.txt", "-o$tmp_hairpin_name.MFE.txt");
unlink "$tmp_hairpin_name.txt";
open TEMPHPMFE, "$tmp_hairpin_name.MFE.txt" or die ("[-] Error: Can't open temp MFE file $tmp_hairpin_name.MFE.txt\n");
my $tmpHPMFE=1;
while(my $tmpMFE = <TEMPHPMFE>){
# say $.;
if ($. == 3 ){
$tmpHPMFE=substr($tmpMFE,-8);
$tmpHPMFE=substr($tmpHPMFE,0,6);
# say $tmpHPMFE;
$tmpHPMFE=$tmpHPMFE+0.0;
# say $tmpHPMFE;
}else{
next;
}
}
close TEMPHPMFE;
unlink "$tmp_hairpin_name.MFE.txt";
##### End of Calculate MFE
if ($tmpHPMFE <= $MFET){
print RSUTCA ">$HID ";
print RSUTCA "$ChrID:$seqstarpos..$seqpos $l3 $2 $3 $4 $tmpHPMFE\n";
print RSUTCA $1,"\n";
# print RSUT "-----------------------------------------\n";
say FASTARESULTCA ">$ChrID"."H$count1.up $ChrID:$seqstarpos..$seqpos";
if ($seqpos<$upstreml){
our $rightfinalseq = substr($seqall,0,$seqpos);
}else{
our $rightfinalseq = substr($seqall,$seqpos-$upstreml,$upstreml);
}
print FASTARESULTCA "$rightfinalseq\n";
print DOWNFACA ">$ChrID"."H$count1.down $ChrID:$seqpos..$seqdownpos\n";
our $downfasta = substr($seqall,$seqpos,$downstreml);
print DOWNFACA "$downfasta\n";
print OUTGFFCA "$ChrID\tEAhelitron\tCDS\t$seqstarpos\t$seqpos\t.\t+\t.\tName=$HID.3;ID=$HID;Parent=$HID;Type=Helitron;Super_Family=Helitron;MFE=$tmpHPMFE\n";
print OUTBEDCA "$ChrID\t".($seqstarpos-1)."\t".($seqpos)."\t$HID\t1\t+\n";
our $TCi=0;
#say our $TCseq='([atgcn]{10}(TC(TCTACTA|T.TACTA.T|T.TACTAC|.{2}TACTACT|T.TAC.ACT|T.TA.TACT|T.TACT.CT|T.T.CTACT|.CTACTA.T|.{9}TATTAAG))[atgcn]{15})';
our $rfsl=length($rightfinalseq);
while($rightfinalseq=~/$TCseq/igc){
$TCi++;
my $TCL=length($1)-25;
my $TCpos=pos($rightfinalseq)-20;
my $TCposstar=$TCpos-$TCL+1;
my $TCgpos=$seqpos-$rfsl+$TCpos;
my $TCgposstar=$seqpos-$rfsl+$TCposstar;
print TCRSUTCA ">$HID.5.$TCi $ChrID:$TCgposstar..$TCgpos $2\n";
print TCRSUTCA "$1\n";
print OUTGFFCA "$ChrID\tEAhelitron\tCDS\t$TCgposstar\t$TCgpos\t.\t+\t.\tName=$HID.5.$TCi;ID=$HID.5.$TCi;Parent=$HID;Type=Helitron;Super_Family=Helitron;MFE=$tmpHPMFE\n";
print TCFARESULTCA ">$HID.5.$TCi $ChrID:$TCgposstar..$seqpos\n";
my $FullHseq=substr($rightfinalseq,$TCposstar-1,$upstreml);
print TCFARESULTCA "$FullHseq\n";
}
$count1++; ## 2023.10.05 move to the last step.
$count1[$ni]++;
}
}
################ deal with plus seqs End#################
################Start TR-seqs#############################
$seqall = TRseq($seqall);
$count2=1;
$count2[$ni]=1;
$count2TMP[$ni]=0;
our $seqalll = length($seqall);
$genomel += $seqalll;
while ($seqall=~ /$testseq/igc){
#while ($seqall =~ /$testseq/igc){
#say $seqfilename;
#say "Chrom:",$AN;
# $count2++; ## 2023.10.05 move to the last step.
# $count2[$ni]++; ## 2023.10.05 move to the last step.
$count2TMP[$ni]++;
#say "No.",$count2;
our $l3=length ($3);
our $l1=length ($1);
our $seqpos=$seqalll-(pos($seqall)-5)+1;
our $seqstarpos=$seqpos+$l1-16;
our $ChrID=$Chrname[$ni];
our $trHID ="tr$ChrID"."H$count2";
#say $trHID;
##### Calculate MFE
#say $HID;
my $tmp_hairpin_name = "cache.$timestamp.$opfn.$trHID.tmp".$count2TMP[$ni];
my $tmp_hairpin_fa = substr($1, 0, -9); # Clip last 9 nt.
open TEMPHP,">$tmp_hairpin_name.txt" or die ("[-] Error: Can't open or create temp file $tmp_hairpin_name.txt\n");
print TEMPHP ">tr$ChrID"."H"."$count2 $ChrID:$seqstarpos..$seqpos $l3 $2 $3 $4\n";
print TEMPHP "$tmp_hairpin_fa\n";
close TEMPHP;
## RNAfold
system("RNAfold", "--noPS", "$tmp_hairpin_name.txt", "-o$tmp_hairpin_name.MFE.txt");
unlink "$tmp_hairpin_name.txt";
open TEMPHPMFE, "$tmp_hairpin_name.MFE.txt" or die ("[-] Error: Can't open temp MFE file $tmp_hairpin_name.MFE.txt\n");
my $tmpHPMFE=1;
while(my $tmpMFE = <TEMPHPMFE>){
# say $.;
if ($. == 3 ){
$tmpHPMFE=substr($tmpMFE,-8);
$tmpHPMFE=substr($tmpHPMFE,0,6);
# say $tmpHPMFE;
$tmpHPMFE=$tmpHPMFE+0.0;
# say $tmpHPMFE;
}else{
next;
}
}
close TEMPHPMFE;
unlink "$tmp_hairpin_name.MFE.txt";
##### End of Calculate MFE
if ($tmpHPMFE <= $MFET){
print RSUTCA ">$trHID $ChrID:$seqstarpos..$seqpos $l3 $2 $3 $4 $tmpHPMFE\n";
print RSUTCA $1,"\n";
# print RSUT "-----------------------------------------\n";
say FASTARESULTCA ">tr$ChrID"."H$count2.up $ChrID:$seqstarpos..$seqpos";
my $trseqpos = pos($seqall)-5;
if($trseqpos<$upstreml){
our $rightfinalseq = substr($seqall,0,$trseqpos);
}else{
our $rightfinalseq = substr($seqall,$trseqpos-$upstreml,$upstreml);
}
say FASTARESULTCA $rightfinalseq;
if ($seqpos<$downstreml) {
print DOWNFA ">tr$ChrID"."H$count2.down $ChrID:$seqpos..1\n";
}else {
my $temppos=$seqpos-$downstreml;
print DOWNFACA ">tr$ChrID"."H$count2.down $ChrID:$seqpos..$temppos\n";
}
#print DOWNFA ">tr$ChrID"."H$count2.down $ChrID:$seqpos..$seqpos-$downstreml\n";
our $downfasta = substr($seqall,$trseqpos,$downstreml);
print DOWNFACA "$downfasta\n";
print OUTGFFCA "$ChrID\tEAhelitron\tCDS\t$seqpos\t$seqstarpos\t.\t-\t.\tName=$trHID.3;ID=$trHID;Parent=$trHID;Type=Helitron;Super_Family=Helitron;MFE=$tmpHPMFE\n";
print OUTBEDCA "$ChrID\t".($seqpos-1)."\t".($seqstarpos)."\t$trHID\t1\t-\n";
our $TCi=0;
#say our $TCseq='([atgcn]{10}(TC(TCTACTA|T.TACTA.T|T.TACTAC|.{2}TACTACT|T.TAC.ACT|T.TA.TACT|T.TACT.CT|T.T.CTACT|.CTACTA.T|.{9}TATTAAG))[atgcn]{15})';
our $rfsl=length($rightfinalseq);
while($rightfinalseq=~/$TCseq/igc){
$TCi++;
my $TCL=length($1)-25;
my $TCpos=pos($rightfinalseq)-20;
my $TCposstar=$TCpos-$TCL+1;
my $TCgpos=$seqpos+$rfsl-$TCpos;
my $TCgposstar=$seqpos+$rfsl-$TCposstar;
print TCRSUTCA ">$trHID.5.$TCi $ChrID:$TCgposstar..$TCgpos $2\n";
print TCRSUTCA "$1\n";
print OUTGFFCA "$ChrID\tEAhelitron\tCDS\t$TCgpos\t$TCgposstar\t.\t-\t.\tName=$trHID.5.$TCi;ID=$trHID.5.$TCi;Parent=$trHID;Type=Helitron;Super_Family=Helitron;MFE=$tmpHPMFE\n";
print TCFARESULTCA ">$trHID.5.$TCi $ChrID:$TCgposstar..$seqpos\n";
my $FullHseq=substr($rightfinalseq,$TCposstar-1,$upstreml);
print TCFARESULTCA "$FullHseq\n";
}
$count2++; ## 2023.10.05 move to the last step
$count2[$ni]++; ## 2023.10.05 move to the last step.
}
}
################ TR-seqs End#############################
$count2[$ni]=$count2[$ni]-1; ## 2023.10.05 move to the last step
$count1[$ni]=$count1[$ni]-1; ## 2023.10.05 move to the last step
print GENOMELENHCA "$Chrname[$ni]\t$seqalll\t$count1[$ni]\t$count2[$ni]\t".($count1[$ni] + $count2[$ni])."\t".($count1[$ni]/$seqalll)*1e6."\t".($count2[$ni]/$seqalll)*1e6."\t".($count1[$ni]+$count2[$ni])/$seqalll*1e6."\n";
# print "$Chrname[$ni]\t$seqalll\t$count1[$ni]\t$count2[$ni]\t".($count1[$ni] + $count2[$ni])."\t".($count1[$ni]/$seqalll)*1e6."\t".($count2[$ni]/$seqalll)*1e6."\t".($count1[$ni]+$count2[$ni])/$seqalll*1e6."\n";
# $countall = $countall + $count1[$ni] + $count2[$ni];
# #$genomel += $seqalll;
# $count1all += $count1[$ni];
# $count2all += $count2[$ni];
# close RUST$ni,">>cache.$Chrname[$ni].3.txt";
# close FASTARESULT$ni,">> cache.$Chrname[$ni].u$upstreml.fas";
# close TCRSUT$ni, ">>cache.$Chrname[$ni].5.txt";
# close TCFARESULT$ni, ">>cache.$Chrname[$ni].5.fa";
# close OUTGFF$ni, ">> cache.$Chrname[$ni].gff3";
close RSUTCA;
close FASTARESULTCA;
close TCRSUTCA;
close TCFARESULTCA;
close OUTGFFCA;
close DOWNFACA;
close OUTBEDCA;
close GENOMELENHCA;
$pm->finish;
}
$pm->wait_all_children;
###################Write the out_put files#############
print "Writing to the final output files.\n";
for (our $ni=0;$ni<$Chri;$ni++){
open RSUTCA,"cache.$Chrname[$ni].3.txt";
open FASTARESULTCA,"cache.$Chrname[$ni].u$upstreml.fa";
open TCRSUTCA, "cache.$Chrname[$ni].5.txt";
open TCFARESULTCA, "cache.$Chrname[$ni].5.fa";
open OUTGFFCA, "cache.$Chrname[$ni].gff3";
open DOWNFACA, "cache.$Chrname[$ni].down$downstreml.fa";
open OUTBEDCA, "cache.$Chrname[$ni].bed";
open GENOMELENHCA, "cache.$Chrname[$ni].len.txt";
print RSUT <RSUTCA>;
print FASTARESULT <FASTARESULTCA>;
print TCRSUT <TCRSUTCA>;
print TCFARESULT <TCFARESULTCA>;
print OUTGFF <OUTGFFCA>;
print DOWNFA <DOWNFACA>;
print OUTBED <OUTBEDCA>;
# print GENOMELENH <GENOMELENHCA>;
while (our $lentemp=<GENOMELENHCA>){
print $lentemp;
print GENOMELENH $lentemp;
my @lencount=split('\t',$lentemp);
$genomel += $lencount[1];
$count1all += $lencount[2];
$count2all += $lencount[3];
$countall += $lencount[4];
}
close RSUTCA;
close FASTARESULTCA;
close TCRSUTCA;
close TCFARESULTCA;
close OUTGFFCA;
close DOWNFACA;
close OUTBEDCA;
close GENOMELENHCA;
unlink "cache.$Chrname[$ni].3.txt";
unlink "cache.$Chrname[$ni].u$upstreml.fa";
unlink "cache.$Chrname[$ni].5.txt";
unlink "cache.$Chrname[$ni].5.fa";
unlink "cache.$Chrname[$ni].gff3";
unlink "cache.$Chrname[$ni].down$downstreml.fa";
unlink "cache.$Chrname[$ni].bed";
unlink "cache.$Chrname[$ni].len.txt";
}
##################End Write files#############
close RSUT;
close FASTARESULT;
close TCRSUT;
close TCFARESULT;
close OUTGFF;
close DOWNFA;
close OUTBED;
# say "$genomel $count1all $count2all $countall";
print GENOMELENH "Whole_genome\t$genomel\t$count1all\t$count2all\t$countall\t".$count1all/$genomel*1e6."\t".$count2all/$genomel*1e6."\t".$countall/$genomel*1e6."\n";
close GENOMELENH;
######################################
#End main
######################################
our $endtime=time();
#say $starttime;
#say $endtime;
printf "Done! %g Sec %g Min\n",$endtime-$starttime,($endtime-$starttime)/60;