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#!/usr/bin/perl -w
die "Usage: $0 TEMPLATE OUTDIR\n" if @ARGV < 2;
my %tools = (
rscu => ['calculate Relative Synonymous Codon Usage (RSCU)','rscu'],
cu => ['calculate codon usage','cu'],
aau => ['calculate Amino Acid Usage (AAU)','aau'],
fop => ['calculate Frequency of OPtimal codons index (FOP)','fop'],
raau => ['calculate Relative Amino Acid Usage (RAAU)','raau'],
tidy => ['clean up sequence in FASTA format','tidy'],
reader => ['output sequence in reader format','reader'],
cutab => ['tabulation of codon usage','cutab'],
cutot => ['tabulation of datasets codon usage','cutot'],
transl => ['conceptual translation of DNA to amino acid','transl'],
bases => ['detailed report of base composition','base','base'],
base3s => ['silent base G+C+A+T calculating program','sil_base'],
dinuc => ['dinucleotide usage of the three codon positions','dinuc'],
cai => ['calculate Codon Adaptation Index (CAI)','cai'],
gc3s => ['GC of synonymous codons 3rd positions','gc3s'],
gc => ['G+C content of gene (all 3 codon positions)','gc'],
cbi => ['calculate Codon Bias Index (CBI)','cbi'],
enc => ['calculate Effective Number of Codons (ENc)','enc']
);
open FILE, $ARGV[0] or die "Could not open file: $!";
$string = join("", <FILE>);
close FILE;
foreach my $tool (keys %tools) {
my $tmpl = $string;
my $uctool = uc $tool;
print @{$tools{$tool}}[0] . "\n";
open(my $fh, '>', "$ARGV[1]/codonw-$tool.1") or die "Could not open output file $!";
$tmpl =~ s/%%TOOLNAME%%/codonw-$tool/g;
$tmpl =~ s/%%CTOOLNAME%%/CODONW-$uctool/g;
$tmpl =~ s/%%TOOLDESC%%/@{$tools{$tool}}[0]/g;
$tmpl =~ s/%%TOOLOPT%%/@{$tools{$tool}}[1]/g;
print $fh "$tmpl";
close $fh;
}
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