20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,65 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::Bin/../../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);
+}