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#!/usr/bin/perl -w
use strict;
use Getopt::Long;
#Convert a raw Rmatrix to a properly formatted phylip matrix. If -t is
#included, reference a esprit tag to sequence identifier to replace
#matrix tag ids with sequence ids. Note that for MOTHUR's bin_seqs we want the
#sequence id to perfectly match sequence database headers....
my ($in_raw_matrix, $esprit_tag_2_seqid_lookup, $outmatrix );
'i=s' => \$in_raw_matrix,
't=s' => \$esprit_tag_2_seqid_lookup,
'o=s' => \$outmatrix,
open( IN, $in_raw_matrix ) || die;
my @inlines = <IN>;
close IN;
open( OUT, ">$outmatrix" ) || die;
my $heads = shift( @inlines); #top line is header, so don't count it
my $ntaxa = @inlines;
print OUT "\t$ntaxa\n";
#Fast format, no lookup needed
unless( defined( $esprit_tag_2_seqid_lookup ) ){
foreach my $line ( @inlines ){
chomp $line;
print OUT "$line\n";
#Convert esprit tag ids to seq ids
open( LOOK, $esprit_tag_2_seqid_lookup ) || die;
my %lookup = ();
chomp $_;
my ($tagid, $seqid, @extra) = split("\t", $_);
$lookup{$tagid} = $seqid;
close LOOK;
foreach my $line( @inlines ){
chomp $line;
if( $line =~ m/^\"(.*)\"/ ){
my $tag = $1 - 1; #R is 1 indexed, esprit is 0 indexed
my $seqid = $lookup{$tag};
$line =~ s/^\"(.*)\"/\"$seqid\"/;
print OUT "$line\n";
warn("Can't replace tag id with sequence id!\n");
close OUT;