Bio-NEXUS

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exec/nexfix.pl  view on Meta::CPAN

    unless ($flags{v}) { 
        open(STDERR, ">> ./$directory/error.log") || die "Couldn't open error log in $directory\n";
    }
    
    # get the time stamp, so it can be reported later
    my $time = localtime time;
    
#    print STDERR "$shortname run on $time\n";
    
    # slurp in the entire NEXUS file
    my $nexus_text = do {local(@ARGV, $/) = $path; <>};
    
    # move the old file to filename.old unless the user has specified 
    # overwriting (-c) or keeping the original file intact (-k)
    move($path, "$path.old") unless ($flags{c} || $flags{k});
    
    # use an alternate filename for the new file if the user specifies keeping the original file
    if ($flags{k}) {$path = "$path.new";}
    
    # split the file into its commands (and their arguments)
    my @commands = split(/;/, $nexus_text);

exec/nextool.pl  view on Meta::CPAN

    my $args = "@args";
    $args =~ s/title\s*=\s*(\w+)//i;    
    my $title = $1;
#    my $block = $nexus->get_block("characters", $title);
    
    die "need column numbers" unless $args;
    
    my $columns;
    if ($args =~ /-f (\S+)/) { # input from file
        my $file = $1;
        $columns = do{ local(@ARGV, $/) = $file; <>};
        $columns =~ s/\n/ /g;
    }else {   # input from command line separated by comma or space
        $columns = $args;
    }
    
    my @columns = @{ &parse_number($columns) };
    if ($command) {
        return $nexus->select_chars(\@columns, $title);
    }else {
        return $nexus->exclude_chars(\@columns, $title);

exec/readin_tcoffee.pl  view on Meta::CPAN

$charblock->get_otuset()->set_otus($otuset);

$charblock->set_taxlabels(keys %{ $scores->{'row'} });
$charblock->write();


## Subroutines ##

sub slurp {
    my ($filename) = @_;
    my $file_contents = do{ local(@ARGV, $/) = $filename; <>};
    return $file_contents;
}

lib/Bio/NEXUS/Tools/NexModifier.pm  view on Meta::CPAN

   my $args = "@args";
   $args =~ s/title\s*=\s*(\w+)//i;    
   my $title = $1;
#    my $block = $nexus->get_block("characters", $title);

   die "need column numbers" unless $args;

   my $columns;
   if ($args =~ /-f (\S+)/) { # input from file
      my $file = $1;
      $columns = do{ local(@ARGV, $/) = $file; <>};
      $columns =~ s/\n/ /g;
   }else {   # input from command line separated by comma or space
      $columns = $args;
   }

   my @columns = @{ &parse_number($columns) };
   if ($command) {
      return $nexus->select_chars(\@columns, $title);
   }else {
      return $nexus->exclude_chars(\@columns, $title);