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for_partial.pm
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236 lines (230 loc) · 8.99 KB
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#plus strand ......A(7)TG-----TGA(21)........;
#minusstrand ......T(7)CA----CAT(21).........;
#perl get_partial.pl /home/xuyong1/IDASM/Divide_Stitch_merge/V5.2/V52P3ToGrassFL.blastn /home/xuyong1/IDASM/Divide_Stitch_merge/V5.2/V52P3_NoFLCorrect_16250.fsa >/home/xuyong1/IDASM/Divide_Stitch_merge/V5.2/partial
package for_partial;
###this packgae get the blastfile and fastafile, predict
use strict;
use Bio::SearchIO;
use warnings;
use get_blast_start_end;
sub codingext {
my($blastfile, $fastafile)=@_;
my %name_seq=name_seq($fastafile);
my $blast= new Bio::SearchIO (-file=>$blastfile, -format=>'blast');
my $kk=0;
while (my $result = $blast->next_result){
my $queryname=$result->query_accession;
my $querylength=$result->query_length;
my $m=0;
my $n=0;
my @hsps=();
my $ii=0;
while(my $hit=$result->next_hit){#######
$ii++;
last if($ii>1);
my $hitlength=$hit->length;
my $hitname=$hit->accession;
my $seq=$name_seq{$queryname};
my $strand=0;
my $i_strand=0;
while (my $hsp = $hit->next_hsp){
$i_strand++;
my $hsplength=$hsp->length('query');
my $similar=$hsp->percent_identity;
next if($similar<40);
my $hit_strand=$hsp->strand('hit');
my $hit_start=$hsp->start('hit');
my $hit_end=$hsp->end('hit');
my $query_start=$hsp->start('query');
my $query_end=$hsp->end('query');
my $cover=$hsplength/$hitlength;
$strand=$hsp->strand('query') if($i_strand==1);
push @hsps, {hit_start=>$hit_start, hit_end=>$hit_end, query_start=>$query_start,
query_end=>$query_end, similar=>$similar};
}#parsing one hit finished
last if($#hsps<0);
my($fhit_start, $fhit_end,$len_hsps, $fquery_start, $fquery_end)=get_blast_start_end::tiling(@hsps);
######### #####if($len_hsps/$hitlength>=0.5){
if($len_hsps/$hitlength>=0.5||$len_hsps>50){
my ($head, $fas)=xts($fhit_start, $fhit_end, $hitlength,
$fquery_start, $fquery_end, $querylength,$strand, $seq, $queryname);
if($head){
$head.=" hitname:".$hitname." HitLength:". $hitlength. " HitHSP:".$fhit_start."_".$fhit_end."\n";
#strand:1 queryLength:929 expect:115_360 QueryHSP:115_360 extension:115_360 hitname:AK250501 HitHSP:
print ">".$head, $fas, "\n";
}
}
}
}#parse blast result;
} #end of main sub;
sub xts{
my($hit_start, $hit_end, $hitlength, $query_start, $query_end, $querylength,$strand,$seq,$queryname)=@_;
my $five_ter=0;
my $three_ter=0;
my $expect_start=0;
my $expect_end=0;
my $fasseq="";
my $five_expect=3*($hit_start-1);#absolute length
my $three_expect=3*($hitlength-$hit_end);#hit seq as reference
if($strand==-1){#minus strand
$expect_start=$query_start-$three_expect;#absolute length
$expect_end=$query_end+$five_expect;
if($query_start>$three_expect){###here utr respresent terminal
my $expect_pos=$query_start-$three_expect;
$five_ter=extension_reverse($hit_start, $hit_end, $query_start, $query_end,
$seq, $querylength, $strand,$expect_pos, $queryname);
}
if($query_start<=$three_expect){
my $uncom=$three_expect-$query_start;
$five_ter="uncomplete in 5' terminal ".$uncom." nt ";
}
if ($hit_start>1&&($querylength-$query_end)>$five_expect){
my $expect_pos=$query_end+$five_expect;
$three_ter=extension_forward($hit_start, $hit_end, $query_start, $query_end,$seq,
$querylength,$strand,$expect_pos, $queryname);
}
if(($querylength-$query_end)<=$five_expect){
my $uncom=$five_expect-($querylength-$query_end);
$three_ter="uncomplete in 3' terminal ".$uncom." nt ";
}
}####strand minus;
if ($strand==1){
$expect_start=$query_start-$five_expect;
$expect_end=$query_end+$three_expect;
if($hit_start>1&&($query_start>$five_expect)){
my $expect_pos=$query_start-$five_expect;
$five_ter=extension_reverse($hit_start, $hit_end, $query_start, $query_end,
$seq, $querylength, $strand,$expect_pos, $queryname);
}
if($hit_start>1&&($query_start<=$five_expect)){
my $uncom=abs($expect_start);
$five_ter="uncomplete in 5' terminal ".$uncom."nt ";
}
if(($querylength-$query_end)>$three_expect){
my $expect_pos=$query_end+$three_expect;
$three_ter=extension_forward($hit_start, $hit_end, $query_start, $query_end,$seq,
$querylength, $strand,$expect_pos, $queryname);
}
if(($querylength-$query_end)<$three_expect){
my $uncom=$expect_end-$query_end;
$three_ter="uncomplete in 3' terminal ".$uncom."nt ";
}
} ###plus strand;
if($hit_start==1){
$five_ter=$query_start if($strand==1);
$three_ter=$query_end if($strand==-1);
}
if($hit_end==$hitlength){
$five_ter=$query_start if($strand==-1);
$three_ter=$query_end if($strand==1);
}
if($five_ter=~/uncomplete/||$three_ter=~/uncomplete/){
my $flcds=$expect_end-$expect_start+1;
my $five_act=0;
my $three_act=0;
$five_act=($five_ter=~/uncomplete/ ? 1 :$expect_start);
$three_act=($three_ter=~/terminal/ ? $querylength : $expect_end);
my $length_act=$three_act-$five_act+1;
my $ratio=$length_act/$flcds * 100;
$fasseq= ">".$queryname." ".$strand. " QueryLength:". $querylength ." expect:".$expect_start."_".$expect_end." "."HSP:".$query_start
."_".$query_end." "."extension: ".$five_ter."||".$three_ter." ratio:".$ratio."%"."\n".$seq."\n";
my $head = $queryname." strand:". $strand." QueryLength:". $querylength ." expect:". $expect_start. "_". $expect_end." QueryHSP:". $query_start
."_".$query_end. " extension:".$five_ter."||".$three_ter." ratio:".$ratio."%";
return ($head, $seq);
}
}
#########################
sub name_seq{
use Bio::SeqIO;
my %name_seq=();
my $infasta= new Bio::SeqIO (-file=>$_[0], -format=>"fasta");
while(my $fasta=$infasta->next_seq){
my $name=$fasta->display_id;
my $seq=$fasta->seq();
$name_seq{$name}=$seq;
}
return (%name_seq);
}
##########################################
sub extension_forward{
my ($hit_start, $hit_end, $query_start, $query_end, $seq, $querylength,$strand,$expect_pos, $queryname)=@_;
my %pos=();
my $scan_start=$expect_pos-30;
my $scan_end=length($seq);
$scan_end=$expect_pos+30 if(($expect_pos+30)<=length($seq));
if($strand==1){
for(my $i=$scan_start;$i<=$scan_end;$i+=3){
my $tri_nt=substr($seq, $i,3);
#print $i, "\t",$tri_nt, "\n";
if($tri_nt=~/TAG|TGA|TAA/){
$pos{$i}=abs($expect_pos-$i);
}
}
if(keys %pos){
my @sorted= sort {$pos{$a} <=> $pos{$b}} (keys %pos);
return ($sorted[0]+3);
}
}
if($strand==-1){
my %pos=();
my $scan_start=$expect_pos-30;
my $scan_end=length($seq);
$scan_end=$expect_pos+30 if(($expect_pos+30)<=length($seq));
for(my $i=$scan_start;$i<=$scan_end;$i+=3){
my $tri_nt=substr($seq, $i,3);
if($tri_nt=~/CAT/){
$pos{$i}=abs($expect_pos-$i);
}
}
if(keys %pos){
my @sorted= sort {$pos{$a} <=> $pos{$b}} (keys %pos);
return ($sorted[0]+3);
}
}
}
######################
sub extension_reverse {
my ($hit_start, $hit_end, $query_start, $query_end,$seq,$querylength, $strand,$expect_pos, $queryname)=@_;
my %pos=();
my $int=int($expect_pos/3);
my $scan_start=$expect_pos-(3*$int);
$scan_start=$expect_pos-30 if(($expect_pos-30)>=0);
if($strand==1){
for(my $i=$scan_start;$i<=($expect_pos+30);$i+=3){
my $tri_nt=substr($seq, $i-1,3);
if($tri_nt=~/ATG/){
$pos{$i}=abs($expect_pos-$i);
}
}
#print "start ",$expect_pos, "\n", join("\t", keys %pos),"\n";
if(keys %pos){
my @sorted= sort {$pos{$a} <=> $pos{$b}} (keys %pos);
return ($sorted[0]);
}
}
if($strand==-1){
for(my $i=$scan_start;$i<=($expect_pos+30);$i+=3){
my $tri_nt=substr($seq, $i-1,3);
if($tri_nt=~/CTA|TCA|TTA/){
$pos{$i}=abs($expect_pos-$i);
}
}
if(keys %pos){
my @sorted= sort {$pos{$a} <=> $pos{$b}} (keys %pos);
return ($sorted[0]);
}
}
}
################
sub rev_comp {
my $seq=$_[0];
my $len=length($seq);
my $five_ter=$_[1];
my $three_ter=$_[2];
my $r_seq=reverse($seq);
$r_seq=~tr/ATGC/TACG/;
my $start=$len-$three_ter+1;
my $end=$len-$five_ter+1;
return ($r_seq, $start, $end);
}
1;