50 lines
975 B
Perl
50 lines
975 B
Perl
|
=pod
|
||
|
|
Solutions to GRPH Rosalind problem
|
||
|
|
Author: Peter Vlasveld
|
||
|
|
=cut
|
||
|
|
|
||
|
|
#!/usr/bin/perl
|
||
|
|
use common::sense;
|
||
|
|
|
||
|
|
#take in data
|
||
|
|
open(IN, "rosalind_grph.txt") or die "Couldn't open input file";
|
||
|
|
my @data = <IN>;
|
||
|
|
close IN;
|
||
|
|
|
||
|
|
#declare variables
|
||
|
|
my (@headers, @DNA, @result);
|
||
|
|
my $temp = "";
|
||
|
|
|
||
|
|
#convert FASTA data into array of DNA strings and headers
|
||
|
|
for (@data){
|
||
|
|
unless (substr($_,0,1) eq '>'){
|
||
|
|
$temp .= substr($_,0,-1);
|
||
|
|
} else {
|
||
|
|
push @headers, substr($_,0,-1);
|
||
|
|
push @DNA, $temp;
|
||
|
|
$temp = "";
|
||
|
|
}
|
||
|
|
}
|
||
|
|
push @DNA, $temp;
|
||
|
|
shift @DNA;
|
||
|
|
#print @headers,"\n",@DNA,"\n";
|
||
|
|
|
||
|
|
#write which headers overlap to @result
|
||
|
|
for my $i (0..$#DNA){
|
||
|
|
for my $j (0..$#DNA){
|
||
|
|
print "$DNA[$i]$DNA[$j]\n";
|
||
|
|
if ($DNA[$i] eq $DNA[$j]) { next; }
|
||
|
|
elsif (substr($DNA[$i],-3) eq substr($DNA[$j],0,3)){
|
||
|
|
push @result, substr($headers[$i],1)." ".substr($headers[$j],1);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
#print result to file
|
||
|
|
open(OUT, ">output.txt") or die "Couldn't open output file";
|
||
|
|
for (@result){
|
||
|
|
print OUT $_,"\n";
|
||
|
|
}
|
||
|
|
close OUT;
|
||
|
|
|