Certainly. Something like the following:
#!/usr/local/bin/perl
use feature qw/say/;
use strict;
use warnings;
open my $FASTAFILE, "<", 'human_fold_25.txt'
or die "Could not open file: $!";
my $sequence = ' ';
my $Ccount = 0;
my $Gcount = 0;
my $identifier = ' ';
while(my $line = <$FASTAFILE>) {
chomp $line;
next if $line =~ m/^\./;
if ($line =~ /^>/) {
$identifier = $line;
} elsif ($line !~ /^\(/) {
$sequence = $line;
$Gcount = $Ccount = 0;
my $sequencelength = length $sequence;
my @nucleotides = split('', $sequence);
foreach my $nuc (@nucleotides) {
if ($nuc eq 'G') {
$Gcount = $Gcount + 1;
} elsif ($nuc eq 'C') {
$Ccount = $Ccount + 1;
}
}
my $GCcontent = ((($Gcount + $Ccount) / $sequencelength) * 100
+);
say "$identifier, $GCcontent";
}
}
close $FASTAFILE or die "Could not close file: $!";
Note I've made a few other changes to your code, namely:
- use strict;, and use warnings;. These are your friends; they'll catch many errors for you, and you should always use them. As a side effect, I've also declared variables with my where necessary.
- use feature qw/say/; it's nicer than print if you want to add a newline anyway, IMO.
- Lexical filehandles ($FASTAFILE vs. FASTAFILE).
- Three-argument form of open.
- Error checking for open and close.
- Slightly more idiomatic handling of lines starting with periods.
- Whitespace changes, to improve readability.
Your code could still be tightened up further, of course. For instance, the entire block following elsif ($line !~ /^\(/) could be reduced to the following:
...
} elsif ($line !~ /^\(/) {
my $GCcount =()= ($line =~ m/(G|C)/g);
say "$identifier, " , ($GCcount / length($line) * 100);
}
...
but since you're still new to Perl, I imagine that wouldn't make as much sense. :)
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