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#!/usr/local/bin/perl -w
# POD docs at end
use strict;
use Carp;
use Data::Stag qw(:all);
use Getopt::Long;
my $parser = "";
my $writer = "";
my $debug;
my $help;
GetOptions(
"help|h"=>\$help,
"parser|format|p=s" => \$parser,
"handler|writer|w=s" => \$writer,
"debug"=>\$debug,
);
if ($help) {
system("perldoc $0");
exit 0;
}
my $joinfield = shift @ARGV;
my ($j1, $j2) = ($joinfield, $joinfield);
if ($joinfield =~ /(.*)=(.*)/) {
$j1 = $1;
$j2 = $2;
}
my ($jn1, $jk1) = splitnodekey($j1);
my ($jn2, $jk2) = splitnodekey($j2);
my $fn1 = shift @ARGV;
my @files = @ARGV;
print "$jn1 $jk1 $jn2 $jk2\n";
my %index = ();
my $idxhandler =
Data::Stag->makehandler(-NOTREE=>1,
$jn2=>sub {
my ($self,$stag) = @_;
my $key = $stag->sget($jk2);
$index{$key} = $stag->duplicate;
$stag;
});
foreach my $fn (@files) {
Data::Stag->parse(-file=>$fn,
-format=>$parser,
-handler=>$idxhandler);
}
if ($debug) {
printf "INDEXED KEYVALS: %d\n", scalar(keys %index);
}
my $jhandler =
Data::Stag->makehandler($jn1=>sub {
my ($self,$stag) = @_;
my $key = $stag->sget($jk1);
my $val = $index{$key};
if ($val) {
$stag->add_species($val->data);
}
$stag;
});
my $whandler =
Data::Stag->chainhandlers([$jn1],
$jhandler,
$writer);
Data::Stag->parse(-file=>$fn1,
-format=>$parser,
-handler=>$whandler);
exit 0;
sub splitnodekey {
my $s = shift;
if ($s =~ /(\w+)\/(.*)/) {
return ($1,$2);
}
return ($s,'');
}
__END__
=head1 NAME
stag-join - joins two stag files together based around common key
=head1 SYNOPSIS
stag-join -w xml country/city_id=capital/capital_id countries.xml capitals.xml
stag-join -w itext gene/tax_id=species/tax_id genedb.itext speciesdb.itext
=head1 DESCRIPTION
Performs a relational-style INNER JOIN between two stag trees; this
effectively merges two files together, based on some kind of ID in the
file
=head1 ARGUMENTS
=over
=item -p|parser FORMAT
FORMAT is one of xml, sxpr or itext, or the name of a perl module
xml assumed as default
=item -w|writer FORMAT
FORMAT is one of xml, sxpr or itext, or the name of a perl module
=back
=head1 LIMITATIONS
currently not event based, so may not be memory efficicent. could be
easily rewritten to be event based
=head1 SEE ALSO
L<Data::Stag>
This script is a wrapper for the method
Data::Stag->ijoin()
=cut
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