#!/usr/bin/perl use warnings; use strict; use Getopt::Std; local $/; our %opts; getopts('hf:', \%opts); die("Usage: uv_mutant.pl -f .gbk\nAdd -h for html output\n") unless $opts{f}; my $file = $opts{f}; my $genome; my $total_mutations; open(FH, $file) or die "File couldn't be opened"; my $contents = ; close(FH); #Extract the entire genome $contents =~ m#ORIGIN(.+?)//#s or die "No genome data found."; $genome = $1; # Remove extraneous characters, make it one big long string to use substr position on it $genome =~ s/[\d\s]+//g; # Calculate total possible mutations while( $genome =~ /[ct](?=[ct])/g ) { $total_mutations++; } #print "\nTotal possible mutations (pyramidine dimerizations): $total_mutations\n\n"; # Extract all the gene definitions, end at protein translation. my @genes; @genes = $contents =~ m#(? $geneid, prod_pro => $gene_product, gene_mutants => $gene_mutations, mutant_prob => $probability }; #printf "%-20s%-10d%-25d%.5f%% %s\n", $gene_name, $geneid, $gene_mutations, $probability, $gene_product; } } if($opts{h}) { html_out($total_mutations, %mutant_genes) }else{ print "UV Mutation (pyramidine dimerization) Analysis\n"; print "Total possible mutations in genome: $total_mutations\n\n"; print "\nGenes sorted by UV mutation probability:\n", "=" x 65, "\n"; foreach (sort by_descending_probability keys %mutant_genes) { printf "%-20s%.5f%% %s\n", $_, $mutant_genes{$_}{mutant_prob}, $mutant_genes{$_}{prod_pro}; } } sub by_descending_probability { $mutant_genes{$b}{mutant_prob} <=> $mutant_genes{$a}{mutant_prob}; } sub html_out { my $total_muts = shift; print "\n\n\n"; print "

UV Mutant Analysis

\n"; print "Total Possible mutations in Genome: $total_muts
\n"; print "Gene mutations sorted by decending probability of mutation
\n"; print "\n\n"; #my %mutant_genes = shift; #Gives an odd numbered hash assignment error when prototyped foreach (sort by_descending_probability keys %mutant_genes) { print "\n"; } print "

Gene	Possible Gene Mutations	Mutation Probability (%)	Gene Product
$_	$mutant_genes{$_}{gene_mutants}	$mutant_genes{$_}{mutant_prob}	$mutant_genes{$_}{prod_pro}

\n"; print "\n"; }