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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use Process_cmd;
my $usage = "\n\n\tusage: $0 Trinity.fasta [out_prefix='GC_content']\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] || "GC_content";
main: {
my $dat_out_file = "$out_prefix.dat";
open(my $ofh, ">$dat_out_file") or die "Error, cannot write to $dat_out_file";
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my $seq_len = length($sequence);
my $gc_count = 0;
while ($sequence =~ /[gc]/ig) {
$gc_count++;
}
my $pct_gc = sprintf("%.2f", $gc_count / $seq_len * 100);
print $ofh join("\t" ,$acc, $pct_gc) . "\n";
}
# generate histogram
my $R_code = <<__eoR__;
data = read.table("$dat_out_file", header=F, row.names=1)
pdf("$dat_out_file.hist.pdf")
hist(data[,1], br=100)
message("\n\nmean: ", sprintf("%.2f", mean(data[,1])), ", median: ", median(data[,1]), "\n\n")
dev.off()
__eoR__
;
{
my $Rscript_file = "$out_prefix.R";
open (my $ofh, ">$Rscript_file") or die "Error, cannot write to file: $Rscript_file";
print $ofh $R_code;
close $ofh;
# run it
my $cmd = "Rscript $Rscript_file";
&process_cmd($cmd);
}
exit(0);
}
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