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#!/usr/bin/perl
use strict;
use warnings;
use File::Basename qw( basename );
use IPC::Run3;
use Getopt::Long::Descriptive;
my $basename = basename $0;
my( $opt, $usage ) = describe_options( <<"END" . 'OPTIONS',
USAGE
$basename [<args>] [<files>]
DESCRIPTION
$basename prepares tests for ChemOnomatopist
END
[ 'author', 'mark output tests with AUTHOR flag' ],
[ 'pubchem', 'treat the input as three-columned PubChem file' ],
[],
[ 'help', 'print usage message and exit', { shortcircuit => 1 } ],
);
if( $opt->help ) {
print $usage->text;
exit;
}
my @lines = <>;
for (@lines) {
s/^\s+//;
s/\s+$//;
my( $smiles, $iupac, $source );
if( $opt->pubchem ) {
( my $id, $iupac, $smiles ) = split /\t/, $_;
$source = "PubChem $id";
} else {
my( $stderr );
$iupac = $_;
run3 [ 'java', '-jar', '/usr/share/java/opsin.jar' ], \$iupac, \$smiles, \$stderr;
$smiles =~ s/\n$//;
}
$iupac =~ s/'/\\'/g;
print "{ smiles => '$smiles', iupac => '$iupac'";
print ', AUTHOR => 1' if $opt->author;
print ' },';
print " # $source" if $source;
print "\n";
}
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