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#!/usr/bin/perl -w
use strict;
while(<>) {
chomp;
my @fields = split / \|\|\| /;
my ($ff, $ee, $aa) = @fields;
die "Expected: foreign ||| target ||| alignments" unless scalar @fields == 3;
my @fs = split /\s+/, $ff;
my @es = split /\s+/, $ee;
my @as = split /\s+/, $aa;
my @oas = ();
push @oas, '0-0';
my $flen = scalar @fs;
my $elen = scalar @es;
for my $ap (@as) {
my ($a, $b) = split /-/, $ap;
die "Bad format in: @as" unless defined $a && defined $b;
push @oas, ($a + 1) . '-' . ($b + 1);
}
push @oas, ($flen + 1) . '-' . ($elen + 1);
print "<s> $ff </s> ||| <s> $ee </s> ||| @oas\n";
}
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