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#!/usr/bin/perl
use strict;
use warnings;
sub calculateACGT {
my $seq=shift(@_);
my $contents=shift(@_);
my $length= length($seq);
my $char="";
for (my $i=0;$i<$length;$i++) {
$char=uc(substr($seq,$i,1));
${$contents}{$char}++;
}
${$contents}{'length'}=$length;
}
sub output {
my $data=shift(@_);
if ((shift(@_))==1) {
print("summary: BASE COUNT ${$data}{'A'} a ${$data}{'C'} c ${$data}{'G'} g ${$data}{'T'} t");
if (${$data}{'N'} > 0) {
print(" ${$data}{'N'} n");
}
if (${$data}{'rest'} > 0) {
print(" ${$data}{'rest'} ?");
}
print("\n");
print("total ${$data}{'length'}bp\n");
print("gc: ${$data}{'gc'}%\n");
}
else {
print("${$data}{'length'} bases.\t${$data}{'name'} ");
print("BASE COUNT ${$data}{'A'} a ${$data}{'C'} c ${$data}{'G'} g ${$data}{'T'} t");
if (${$data}{'N'} > 0) {
print(" ${$data}{'N'} n");
}
if (${$data}{'rest'} > 0) {
print(" ${$data}{'rest'} ?");
}
print("\n");
}
}
sub main {
my $usage="";
my $seqfilename="";
my $seq="";
+my %totaldata=(A=>0,C=>0,G=>0,T=>0,N=>0,rest=>0,gc=>0);
$usage .= "$0 -- count the a,c,g,t \n";
$usage .= "\n";
$usage .= "Usage: $0 seq-file\n";
$usage .= "\n";
if (scalar(@ARGV) < 1) {
die "\n$usage";
}
$seqfilename = $ARGV[0];
open(FASTA, "<$seqfilename") || die "Couldn't open $seqfilename\n";
$/="\n>";
while(<FASTA>) {
my %data=(A=>0,C=>0,G=>0,T=>0,N=>0); # initialize counts to 0
/[>]*(.*)\n/;
$data{'name'}= $1;
$seq = $';
$data{'name'}=~ s/\s+.*//;
$seq =~ s/>//;
$seq =~ s/\n//g;
&calculateACGT($seq,\%data);
$data{'rest'}=$data{'length'}-$data{'A'}-$data{'T'}-$data{'G'}-$data{'C'}-$data{'N'};
foreach my $key ("A","C","T","G","N","rest") {
$totaldata{$key} += $data{$key};
}
&output(\%data,0);
}
my $sum=$totaldata{'T'}+$totaldata{'G'}+$totaldata{'A'}+$totaldata{'C'};
$totaldata{'length'}=$totaldata{'N'}+$totaldata{'rest'}+$sum;
$totaldata{'gc'}=($totaldata{'C'}+$totaldata{'G'})/$sum if ($sum>0);
&output(\%totaldata,1);
}
&main;
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