Radha Agarkar
A Bioinformatician
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Count GC Content in nucleotide sequence with Perl
By Radha Agarkar 3143 days ago
#!/usr/bin/perl -w
### Usage: get_gc_content.pl <fasta file> ###
#---------------------------------------------------------------------------------------------------------------------------
#Deal with passed parameters
#---------------------------------------------------------------------------------------------------------------------------
if ($#ARGV == -1) {
usage();
exit;
}
$fasta_file = $ARGV[0];
$out_file = "gc_out.txt";
unless ( open(IN, "$fasta_file") ) {
print "Got a bad fasta file: $fasta_file\n\n";
exit;
}
unless ( open(OUT, ">$out_file") ) {
print "Couldn't create $out_file\n";
exit;
}
print "Parameters:\nfasta file = $fasta_file\noutput file = $out_file\n\n";
#---------------------------------------------------------------------------------------------------------------------------
#The main event
#---------------------------------------------------------------------------------------------------------------------------
print OUT "ID\t% GCContent\tTotal Count\tG Count\tC Count\tA Count\tT Count\n";
$seq = "";
while (<IN>) {
chomp;
if (/^>/) {
#finish up previous line.
if (length($seq) > 0) {
&process_it;
}
#start new line.
$id = $_;
$id =~ s/^>(.+?)\s.+$/$1/g;
print OUT "$id\t";
}
else {
$seq = $seq . $_;
}
}
#finish up last line.
&process_it;
close(IN);
close(OUT);
sub usage {
$0 get_gc_content.pl <fasta file>
}
sub process_it {
@letters = split(//, $seq);
$gccount = 0;
$totalcount = 0;
$acount = 0;
$tcount = 0;
$gcount = 0;
$ccount = 0;
foreach $i (@letters) {
if (lc($i) =~ /[a-z]/) {
$totalcount++;
}
if (lc($i) eq "g" || lc($i) eq "c") {
$gccount++;
}
if (lc($i) eq "a") {
$acount++;
}
if (lc($i) eq "t") {
$tcount++;
}
if (lc($i) eq "g") {
$gcount++;
}
if (lc($i) eq "c") {
$ccount++;
}
}
if ($totalcount > 0) {
$gccontent = (100 * $gccount) / $totalcount;
}
else {
$gccontent = 0;
}
print OUT "$gccontent\t$totalcount\t$gcount\t$ccount\t$acount\t$tcount\n";
$seq = "";
}
