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Concatenation.pl
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4322 lines (1698 loc) · 67.4 KB
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#!/usr/bin/perl -w
open(SEQFILE, "ScORFs.txt")||die "opening file $!";
@ORFarray = <SEQFILE>;
close (SEQFILE);
#this segment of code reads each line of the file, defining ORFs details, into an array
@NEWDATA=();
open (RESULTS, ">>results_file.txt") ||die "cannot open results.txt: $!";
@NEWDATA = <RESULTS>;
for($index=0; $index<@ORFarray; $index++){
$gene = $ORFarray [$index];
#this 'for' loop takes each line of sequence details in turn out of the array ready for processing
$findtext = index ($gene, ">" , 0);
# finds out where the letter Y is, defining the beginning of the Scer yeast name
$scername= substr ($gene,$findtext,8);
# extracts the Scer gene name
$ATGregion = index ($gene, "???", 0);
$ORFseq = substr ($gene, $ATGregion+3);
$genelen = length ($ORFseq) -2;
#measures length of gene sequence
print "$scername \t $genelen \n";
my $len = 3;
$gene = $ORFseq;
for (my $ORFcod = 1; $ORFcod <= length $ORFseq; $ORFcod += ($len)) {
$fsitectt1 = "CTTACG";
$fsitectt2 = "CTTTCG";
$fsitectt3 = "CTTCGG";
$fsitectt4 = "CTTAGG";
$fsitectt5 = "CTTCTC";
$fsitectt6 = "CTTCAG";
$fsitectt7 = "CTTAGT";
$fsiteggg1 = "GGGACG";
$fsiteggg2 = "GGGTCG";
$fsiteggg3 = "GGGCGG";
$fsiteggg4 = "GGGAGG";
$fsiteggg5 = "GGGCTC";
$fsiteggg6 = "GGGCAG";
$fsiteggg7 = "GGGAGT";
$fsitegcg1 = "GCGACG";
$fsitegcg2 = "GCGTCG";
$fsitegcg3 = "GCGCGG";
$fsitegcg4 = "GCGAGG";
$fsitegcg5 = "GCGCTC";
$fsitegcg6 = "GCGCAG";
$fsitegcg7 = "GCGAGT";
$fsiteccg1 = "CCGACG";
$fsiteccg2 = "CCGTCG";
$fsiteccg3 = "CCGCGG";
$fsiteccg4 = "CCGAGG";
$fsiteccg5 = "CCGCTC";
$fsiteccg6 = "CCGCAG";
$fsiteccg7 = "CCGAGT";
$fsitecuc1 = "CTCACG";
$fsitecuc2 = "CTCTCG";
$fsitecuc3 = "CTCCGG";
$fsitecuc4 = "CTCAGG";
$fsitecuc5 = "CTCCTC";
$fsitecuc6 = "CTCCAG";
$fsitecuc7 = "CTCAGT";
$fsiteagg1 = "AGGACG";
$fsiteagg2 = "AGGTCG";
$fsiteagg3 = "AGGCGG";
$fsiteagg4 = "AGGAGG";
$fsiteagg5 = "AGGCTC";
$fsiteagg6 = "AGGCAG";
$fsiteagg7 = "AGGAGT";
$fsitecug1 = "CTGACG";
$fsitecug2 = "CTGTCG";
$fsitecug3 = "CTGCGG";
$fsitecug4 = "CTGAGG";
$fsitecug5 = "CTGCTC";
$fsitecug6 = "CTGCAG";
$fsitecug7 = "CTGAGT";
my $codon = substr ($ORFseq, $ORFcod - 1, $len);
$sixnt = substr ($ORFseq, $ORFcod - 1, $len +3);
$position = ($ORFcod + (length $sixnt) - 1);
%pos = ($sixnt => $position);
if ($sixnt eq $fsitectt1) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt2) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt3) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt4) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt5) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt6) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsitectt7) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsiteggg1) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsiteggg2) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsiteggg3) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
}
push (@NEWDATA, $a[0]);
}
shift @a;
if ($sixnt eq $fsiteggg4) {
$newstart = index ($gene, "???", 0);
$newseq = substr ($gene, $newstart+($pos{$sixnt})-1);
$newseqlen = length($newseq);
for ($stop =0; $stop <= $newseqlen; $stop = $stop += ($len)){
$stopsite1 = "TAA";
$stopsite2 = "TAG";
$stopsite3 = "TGA";
$newcodon = substr($newseq, $stop, $len);
$newposition = ($stop + (length $newcodon));
%newpos = ($newcodon => $newposition);
if ($newcodon eq $stopsite1 ){
$stopsite = index ($newcodon, $stopsite1);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a,"$stopseq");
}
elsif ($newcodon eq $stopsite2) {
$stopsite = index ($newcodon, $stopsite2);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );
$stop1 = $newposition;
push (@a, "$stopseq");
}
elsif ($newcodon eq $stopsite3) {
$stopsite = index ($newcodon, $stopsite3);
$stopseq = substr ($newseq,$stopsite,$newpos{$newcodon} );