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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
my $usage = "usage: $0 transcripts_file [top_strand_only]\n\n";
my $transcripts_file = $ARGV[0] or die $usage;
my $top_strand_only_flag = $ARGV[1] || 0;
main: {
my %base_counter;
my $fasta_reader = new Fasta_reader($transcripts_file);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = uc $seq_obj->get_sequence();
&count_bases($sequence, \%base_counter);
unless ($top_strand_only_flag) {
$sequence = &reverse_complement($sequence);
&count_bases($sequence, \%base_counter);
}
}
my $sum = 0;
foreach my $count (values %base_counter) {
$sum += $count;
}
foreach my $base (sort keys %base_counter) {
my $count = $base_counter{$base};
my $ratio = $count/$sum;
print join("\t", $base, $count, sprintf("%.3f", $ratio)) . "\n";
}
exit(0);
}
####
sub count_bases {
my ($sequence, $base_counter_href) = @_;
my @chars = split(//, $sequence);
foreach my $char (@chars) {
if ($char =~ /[GATC]/) {
$base_counter_href->{$char}++;
}
}
return;
}
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