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dimer.pm
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dimer.pm
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require "$Bin/score.pm";
#my $min_tm_omega = 17;
my $min_tm_omega = 14;
my $min_tm_omega_noindel = 14;
#my $min_tm_omega_noindel = -15;
my $min_tm_map=10;
my $min_tm_map_noindel=0;
my $min_tm_meet = -50;
my $min_tm_amp = 29; ##Dis-7:26
my $min_meetlen=3; ## min end3 match len when Enddimer
my $min_amplen=15;
#Example:
#mv: ##|||||||||||||*|||||**-|||
#SEQ TT A AT- ----
#SEQ TGGGTGGTGCTAC TCTTC AAT
#STR ACCCACCACGATG AGAAG TTA
#STR AACCGTCCCAACCCCCAACACACCCCCC G AGT AGGA
#mv: ###|||*|*|||**^^^^||||||*||||||||||##
#SEQ ATA A G GGTTTC C AC---
#SEQ AAT A CCT AACCCT TAATTCTTGC
#STR TTA T GGA TTGGGA ATTAAGAACG
#STR AACTGAAATCTTCTTCTCTCCGACAGG G G AA---- C ATTCC
### return:
## pright: primer end3 length of non-mapped
## tleft: template end3 length of non-mapped
## amplen: primer amplified length, ie. template end5 length of non-mapped
## mlen3: primer end3 mapped length
## len: product length
## msum: mapped crowd sum
sub dimer_amplify{
my ($info)=@_;
if(!defined $info || $info eq ""){
return(-100, -1, -1,-1, -1, -1, -1);
}
my ($head,@line) = split /\n/, $info;
if(!defined $head){
print $info,"\n";
die;
}
my ($tm)=$head=~/t = (\S+)/;
if(!defined $tm){
print "yes:\n";
print $info,"\n";
print $head,"\n";
die;
}
$line[0]=~s/SEQ\t//;
$line[1]=~s/SEQ\t//;
$line[2]=~s/STR\t//;
$line[3]=~s/STR\t//;
my @punmap = split //, $line[0];
my @pmap = split //, $line[1];
my @tunmap = split //, $line[3];
my ($tleft, $tright, $pleft, $pright)=(0,0,0,0);
## trim end
for(my $i=0; $i<@punmap; $i++){
last if($pmap[$i] ne " ");
if($punmap[$i] ne " "){
$pleft++;
}
if($tunmap[$i] ne " "){
$tleft++;
}
}
for(my $i=$#punmap; $i>0; $i--){
last if($pmap[$i] ne " ");
if($punmap[$i] ne "-"){
$pright++;
}
if($tunmap[$i] ne "-"){
$tright++;
}
}
## amplify length
my $amplen=$tright;
## end3 map length
$line[1]=~s/^\s+//;
my @maps=split /\s+/, $line[1];
my $msum=scalar @maps;
my $mlen3=length($maps[-1]);
my @unmaps=split /\s+/, $line[0];
if($mlen3<=2){## not really map
my $unmap;
if($amplen>0){## $unmaps[-1] is "---"
$unmap=$unmaps[-2];
$unmap=~s/\-//g;
$pright=$mlen3+length($unmap);
}else{
$unmap=$unmaps[-1];
$unmap=~s/\-//g;
$pright=$mlen3+length($unmap);
}
if(defined $maps[-2]){
$mlen3=length($maps[-2]);
}
}
## indel
my $indel=0;
pop @unmaps;
my @tunmaps=split /\s+/, $line[3];
my @unmapall=(@unmaps, @tunmaps);
for(my $i=0; $i<@unmapall; $i++){
if($unmapall[$i]=~/\-\-/){
$indel++;
}
}
##
my $len = length $line[0];
return ($tm, $pright, $tleft, $amplen, $mlen3, $len, $msum, $indel);
}
sub judge_amplify_endmeet{
my ($tm, $end31, $end32, $mlen3)=@_;
my $is_amplify=0;
my $type = "NoAmplify";
my $eff=0;
my @tm;
if($end31==0 && $end32==0 && $mlen3>=$min_meetlen){
$is_amplify=1;
@tm=(10,100,-50,100,-50,100); #$minb, $maxb, $min, $max, $minl, $maxl
$eff=&score_growth_curve($tm, 1, @tm);
$type = "AmpEndMeet";
}
return ($is_amplify, $type, $eff);
}
sub judge_amplify{
my ($tm, $end31, $end32, $amplen, $mlen3, $msum, $indel)=@_;
my $type="NoAmplify";
my $eff=0;
my @tm;
### judge is amplify or not
if($end31==0 && $end32==0){
if($msum==1){
@tm=(10,100,$min_tm_meet-1,100,$min_tm_meet-1,100); #$minb, $maxb, $min, $max, $minl, $maxl
$eff=&score_growth_curve($tm, 1, @tm);
$type = "AmpEndMeet";
}else{
if($indel==0){
@tm=(20,100,$min_tm_map_noindel-1,100,$min_tm_map_noindel-1,100);
}else{
@tm=(30,100,$min_tm_map,100,$min_tm_map,100);
}
$eff=&score_growth_curve($tm, 1, @tm);
$type = "AmpEndMap";
}
}elsif($end31<=1 || $end32<=1){
if($amplen>=$min_amplen){
if($indel==0){
@tm=(20,100,$min_tm_omega_noindel-1,100,$min_tm_omega_noindel-1,100);
}else{
@tm=(30,100,$min_tm_omega-1,100,$min_tm_omega-1,100); #$minb, $maxb, $min, $max, $minl, $maxl
}
my @alen=(30,100,$min_amplen-1,100,$min_amplen-1,100);
$eff=&score_growth_curve($tm, 1, @tm) * &score_growth_curve($amplen, 1, @alen);
if($eff>0){
$type = "AmpOmega";
}
}else{
if($tm>=$min_tm_amp){
if($indel==0){
@tm=(50,100,25,100,25,100);
}else{
@tm=(60,100,40,100,40,100);
}
$eff=&score_growth_curve($tm, 1, @tm);
$type = "AmpEachOther";
}
}
}
my $is_amplify=0;
if($type ne "NoAmplify"){
$is_amplify=1;
}
return($is_amplify, $type, $eff);
}
#sub efficiency_dimer{
# my ($tm, $pright, $tleft)=@_;
# my @etm=(0, 100, -30, 100);
# my $eff_tm = &score_single($tm, 1, @etm);
# $eff_tm = $eff_tm>0? $eff_tm: 0;
#
# my @
#
#}
1;