#!/usr/bin/env perl

use strict;
use warnings;

my $seen;

while ( <> ) {
	next unless /^\d/;

	s/\s*$//;

	next unless m/		# [file1]	[file2]
		^
		(\S+)		# PeptideID	PeptideID
		\s+
		(\S+)		# ProteinID	SpectrumID
		(?:
			\s+
			(\S+)	# -----		Sequence
		)?
		$
	/x;

	if ( $3 ) {
		$seen->{$1}->{SpectrumID} = $2;
		$seen->{$1}->{Sequence}  = $3;
	} else {
		push @{ $seen->{$1}->{ProteinID} }, $2;
	}
}

sub frmt {
	print join("\t", @_) . "\n";
}

frmt qw( PeptideID ProteinID SpectrumID Sequence );

foreach my $k ( sort { $a <=> $b } keys %{ $seen } ) {
	foreach my $p ( @{ $seen->{$k}->{ProteinID} } ) {
		frmt $k, $p, $seen->{$k}->{SpectrumID}, $seen->{$k}->{Sequence};
	} 
}