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#!/usr/bin/perl -w
%names = ("alignformats" => "AlignFormats",
"assemblyformats" => "AssemblyFormats",
"codonformats" => "CodonFormats",
"featformats" => "FeatFormats",
"ontologyformats" => "OntologyFormats",
"refseqformats" => "RefseqFormats",
"reportformats" => "ReportFormats",
"resourceformats" => "ResourceFormats",
"seqformats" => "SeqFormats",
"seqfeatformats" => "SeqfeatFormats",
"taxonformats" => "TaxonFormats",
"textformats" => "TextFormats",
"urlformats" => "UrlFormats",
"variationformats" => "VariationFormats",
"xmlformats" => "XmlFormats",
"assemblyinformats" => "AssemblyInFormats",
"codoninformats" => "CodonInFormats",
"featinformats" => "FeatInFormats",
"ontologyinformats" => "OntologyInFormats",
"refseqinformats" => "RefseqInFormats",
"resourceinformats" => "ResourceInFormats",
"seqinformats" => "SeqInFormats",
"seqfeatinformats" => "SeqfeatInFormats",
"taxoninformats" => "TaxonInFormats",
"textinformats" => "TextInFormats",
"urlinformats" => "UrlInFormats",
"variationinformats" => "VariationInFormats",
"xmlinformats" => "XmlInFormats",
"gcfiles" => "GeneticCodeFiles",
"localfiles" => "LocalFiles",
"graphicsdevices" => "GraphicsDevices",
"drcat" => "Drcat",
"edam" => "Edam",
"go" => "Go",
"taxon" => "Taxon",
"jaspfiles" => "JasparFiles",
"refiles" => "RebaseFiles",
"jison-programs" => "JonIsonPrograms",
);
open (VERS, "embossversion -full -auto|") || die "Cannot run embossversion";
while (<VERS>) {
if(/InstallDirectory: +(\S+)/) {
$installtop = $1;
$installtop =~ s/\/$//;
}
if(/BaseDirectory: +(\S+)/) {
$distribtop = $1;
$distribtop =~ s/\/$//;
}
}
close VERS;
$docdir = "$distribtop/doc/programs/master/emboss/apps";
$docinc = "$docdir/inc";
opendir(INC, $docinc);
while ($file = readdir(INC)) {
if($file =~ /(^[^.]+)[.]ione$/) {
$newname = "Short".ucfirst($1);
system "cp $docinc/$file $newname";
$newname = "Options".ucfirst($1);
system "acdtable $1 -verbose 2> x.x";
system "wikifytable.pl x.x > $newname";
system "rm x.x";
$newname = ucfirst($1);
system "wikifyhtml.pl $docdir/$1.html > $newname.wiki";
}
if($file =~ /(^[^.]+)[.]isee$/) {
$newname = "Seealso".ucfirst($1);
system "wikifyseealso.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]usage$/) {
$newname = "Example".ucfirst($1);
system "wikifyusage.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]input$/) {
$newname = "Input".ucfirst($1);
system "wikifyusage.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]output$/) {
$newname = "Output".ucfirst($1);
system "wikifyusage.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]comment$/) {
$newname = "Comment".ucfirst($1);
system "wikifyhtml.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]history$/) {
$newname = "History".ucfirst($1);
system "wikifyhtml.pl $docinc/$file > $newname";
}
if($file =~ /(^[^.]+)[.]ihtml$/) {
if(defined($names{$1})) {$newname = $names{$1}}
else{
print "ihtml file $1 has no name\n";
$newname = ucfirst($1);
next;
}
system "wikifyhtml.pl $docinc/$file > $newname";
}
}
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