67 lines
1.3 KiB
Perl
67 lines
1.3 KiB
Perl
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=pod
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Solution to GC Rosalind problem
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Author: Peter Vlasveld
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=cut
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#!/usr/bin/perl
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use strict;
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use warnings;
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#take in data from file
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open(IN, "rosalind_gc.txt") or die "Couldn't open input file";
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my @data = <IN>;
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close IN;
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#declare variables
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my @ID;
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my @sequences;
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my @tempArr;
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my $finalID;
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my $finalPerc = 0;
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#add first @data line to @ID
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$ID[0] = $data[0];
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#loop through 1..$#data
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for (1..$#data){
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#when a line starts with >,
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if (substr($data[$_],0,1) eq '>'){
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#add it to @ID, join the temp array and add it to @sequences
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push @ID, $data[$_];
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my $temp = join ('', @tempArr);
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push @sequences, $temp;
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@tempArr = undef;
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} else {
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#add line to temp array
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push @tempArr, $data[$_];
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}
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}
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#join last temp and add to sequences
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my $temp = join('', @tempArr);
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push @sequences, $temp;
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#loop through @sequences
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for (0..$#sequences){
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$sequences[$_] =~ s/\s//g;
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print $sequences[$_];
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#declare percentage
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my $percentage;
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my $GC;
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my $total = length $sequences[$_];
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#determine percentage of GC in the sequence
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$GC = ($sequences[$_] =~ tr/GC//);
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$percentage = ($GC/$total)*100;
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print "$percentage\n";
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#if percentage is greater than finalPerc, then finalPerc eq percentage and finalID eq ID
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if ($percentage>$finalPerc) {
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$finalPerc = $percentage;
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$finalID = $ID[$_];
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}
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}
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#output id and percent
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printf("%s%f\n", $finalID, $finalPerc);
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