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In addition this code fails when there are spaces before the start of the phylip header:
sub _check_taxa_compatible {
my $tre = shift;
my $aln = shift;
my $R = Statistics::R->new();
my $utility_r_functions = get_utility_R_functions();
my $cmds = <<EOF;
.libPaths( c( .libPaths(), "/travis_R_lib") )
$utility_r_functions
tre <- read.tree("$tre")
dat <- read.delim("$aln",sep="\ ",stringsAsFactors =F)
datx <- dat[[1]]
tret <- tre[[2]]
se <- setequal(datx,tret)
se
EOF
my $r_out = $R->run($cmds);
if($r_out ! 'TRUE') {
warn " constraint tree and alignment have some difference in taxa\n";
warn " please verify that all taxa names are exactly identical and \n";
die " present in both the alignment and constraint \n";
}
}
current warning is that taxa dont match up, difficult to sort out.
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