[scpubgit/stemmatology.git] / lib / Text / Tradition / StemmaUtil.pm

package Text::Tradition::StemmaUtil;

use strict;
use warnings;
use Exporter 'import';
use vars qw/ @EXPORT_OK /;
use Bio::Phylo::IO;
use Encode qw( decode_utf8 );
use File::chdir;
use File::Temp;
use File::Which;
use Graph;
use Graph::Reader::Dot;
use IPC::Run qw/ run binary /;
use Text::Tradition::Error;
@EXPORT_OK = qw/ character_input phylip_pars parse_newick newick_to_svg /;

=head1 NAME

Text::Tradition::StemmaUtil - standalone utilities for distance tree calculations

=head1 DESCRIPTION

This package contains a set of utilities for running phylogenetic analysis on
text collations.

=head1 SUBROUTINES

=head2 character_input( $alignment_table )

Returns a character matrix string suitable for Phylip programs, which 
corresponds to the given alignment table.  See Text::Tradition::Collation 
for a description of the alignment table format.

=cut

sub character_input {
    my $table = shift;
    my $character_matrix = _make_character_matrix( $table );
    my $input = '';
    my $rows = scalar @{$character_matrix};
    my $columns = scalar @{$character_matrix->[0]} - 1;
    $input .= "\t$rows\t$columns\n";
    foreach my $row ( @{$character_matrix} ) {
        $input .= join( '', @$row ) . "\n";
    }
    return $input;
}

sub _make_character_matrix {
    my( $table ) = @_;
    # Push the names of the witnesses to initialize the rows of the matrix.
    my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } 
    				@{$table->{'alignment'}};
    foreach my $token_index ( 0 .. $table->{'length'} - 1) {
        # First implementation: make dumb alignment table, caring about
        # nothing except which reading is in which position.
        my @pos_readings = map { $_->{'tokens'}->[$token_index] }
        						@{$table->{'alignment'}};
        my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;
        my @chars = _convert_characters( \@pos_text );
        foreach my $idx ( 0 .. $#matrix ) {
            push( @{$matrix[$idx]}, $chars[$idx] );
        }
    }
    return \@matrix;
} 

# Helper function to make the witness name something legal for pars

sub _normalize_witname {
    my( $witname ) = @_;
    $witname =~ s/\s+/ /g;
    $witname =~ s/[\[\]\(\)\:;,]//g;
    $witname = substr( $witname, 0, 10 );
    return sprintf( "%-10s", $witname );
}

sub _convert_characters {
    my $row = shift;
    # This is a simple algorithm that treats every reading as different.
    # Eventually we will want to be able to specify how relationships
    # affect the character matrix.
    my %unique = ( '__UNDEF__' => 'X',
                   '#LACUNA#'  => '?',
                 );
    my %count;
    my $ctr = 0;
    foreach my $word ( @$row ) {
        if( $word && !exists $unique{$word} ) {
            $unique{$word} = chr( 65 + $ctr );
            $ctr++;
        }
        $count{$word}++ if $word;
    }
    # Try to keep variants under 8 by lacunizing any singletons.
    if( scalar( keys %unique ) > 8 ) {
		foreach my $word ( keys %count ) {
			if( $count{$word} == 1 ) {
				$unique{$word} = '?';
			}
		}
    }
    my %u = reverse %unique;
    if( scalar( keys %u ) > 8 ) {
        warn "Have more than 8 variants on this location; phylip will break";
    }
    my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
    return @chars;
}

=head2 phylip_pars( $character_matrix )

Runs Phylip Pars on the given character matrix.  Returns results in Newick format.

=cut

sub phylip_pars {
	my( $charmatrix ) = @_;
    # Set up a temporary directory for all the default Phylip files.
    my $phylip_dir = File::Temp->newdir();
    # $phylip_dir->unlink_on_destroy(0);
    # We need an infile, and we need a command input file.
    open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
    print MATRIX $charmatrix;
    close MATRIX;

    open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
    ## TODO any configuration parameters we want to set here
#   U                 Search for best tree?  Yes
#   S                        Search option?  More thorough search
#   V              Number of trees to save?  100
#   J     Randomize input order of species?  No. Use input order
#   O                        Outgroup root?  No, use as outgroup species 1
#   T              Use Threshold parsimony?  No, use ordinary parsimony
#   W                       Sites weighted?  No
#   M           Analyze multiple data sets?  No
#   I            Input species interleaved?  Yes
#   0   Terminal type (IBM PC, ANSI, none)?  ANSI
#   1    Print out the data at start of run  No
#   2  Print indications of progress of run  Yes
#   3                        Print out tree  Yes
#   4          Print out steps in each site  No
#   5  Print character at all nodes of tree  No
#   6       Write out trees onto tree file?  Yes
    print CMD "Y\n";
    close CMD;

    # And then we run the program.
    my $program = File::Which::which( 'pars' );
    unless( -x $program ) {
		throw( "Phylip pars not found in path" );
    }

    {
        # We need to run it in our temporary directory where we have created
        # all the expected files.
        local $CWD = $phylip_dir;
        my @cmd = ( $program );
        run \@cmd, '<', 'cmdfile', '>', '/dev/null';
    }
    # Now our output should be in 'outfile' and our tree in 'outtree',
    # both in the temp directory.

    my @outtree;
    if( -f "$phylip_dir/outtree" ) {
        open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
        @outtree = <TREE>;
        close TREE;
    }
    return join( '', @outtree ) if @outtree;

	# If we got this far, we are about to throw an error.
    my @error;
    if( -f "$phylip_dir/outfile" ) {
        open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
        @error = <OUTPUT>;
        close OUTPUT;
    } else {
        push( @error, "Neither outtree nor output file was produced!" );
    }
    throw( join( '', @error ) );
}

=head2 parse_newick( $newick_string )

Parses the given Newick tree(s) into one or more undirected Graph objects.

=cut

sub parse_newick {
    my $newick = shift;
    my @trees;
    # Parse the result into a tree
    my $forest = Bio::Phylo::IO->parse( 
        -format => 'newick',
        -string => $newick,
        );
    # Turn the tree into a graph, starting with the root node
    foreach my $tree ( @{$forest->get_entities} ) {
        push( @trees, _graph_from_bio( $tree ) );
    }
    return \@trees;
}

=head2 newick_to_svg( $newick_string )

Uses the FigTree utility (if installed) to transform the given Newick tree(s)
into a graph visualization.

=cut

sub newick_to_svg {
	my $newick = shift;
    my $program = File::Which::which( 'figtree' );
    unless( -x $program ) {
		throw( "FigTree commandline utility not found in path" );
    }
    my $svg;
    my $nfile = File::Temp->new();
    print $nfile $newick;
    close $nfile;
	my @cmd = ( $program, '-graphic', 'SVG', $nfile );
    run( \@cmd, ">", binary(), \$svg );
    return decode_utf8( $svg );
}

sub _graph_from_bio {
    my $tree = shift;
    my $graph = Graph->new( 'undirected' => 1 );
    # Give all the intermediate anonymous nodes a name.
    my $i = 0;
    foreach my $n ( @{$tree->get_entities} ) {
        next if $n->get_name;
        $n->set_name( $i++ );
    }
    my $root = $tree->get_root->get_name;
    $graph->add_vertex( $root );
    _add_tree_children( $graph, $root, $tree->get_root->get_children() );
    return $graph;
}

sub _add_tree_children {
    my( $graph, $parent, $tree_children ) = @_;
    foreach my $c ( @$tree_children ) {
        my $child = $c->get_name;
        $graph->add_vertex( $child );
        $graph->add_path( $parent, $child );
        _add_tree_children( $graph, $child, $c->get_children() );
    }
}

sub throw {
	Text::Tradition::Error->throw( 
		'ident' => 'StemmaUtil error',
		'message' => $_[0],
		);
}

1;

=head1 LICENSE

This package is free software and is provided "as is" without express
or implied warranty.  You can redistribute it and/or modify it under
the same terms as Perl itself.

=head1 AUTHOR

Tara L Andrews E<lt>aurum@cpan.orgE<gt>
Commit	Line	Data
68454b71	1	package Text::Tradition::StemmaUtil;
	2
	3	use strict;
	4	use warnings;
	5	use Exporter 'import';
	6	use vars qw/ @EXPORT_OK /;
b02332ca	7	use Bio::Phylo::IO;
27e2a8fe	8	use Encode qw( decode_utf8 );
b02332ca	9	use File::chdir;
	10	use File::Temp;
	11	use File::Which;
	12	use Graph;
	13	use Graph::Reader::Dot;
	14	use IPC::Run qw/ run binary /;
edac47cc	15	use Text::Tradition::Error;
9457207b	16	@EXPORT_OK = qw/ character_input phylip_pars parse_newick newick_to_svg /;
68454b71	17
027d819c	18	=head1 NAME
	19
	20	Text::Tradition::StemmaUtil - standalone utilities for distance tree calculations
	21
	22	=head1 DESCRIPTION
	23
	24	This package contains a set of utilities for running phylogenetic analysis on
	25	text collations.
	26
	27	=head1 SUBROUTINES
	28
9457207b	29	=head2 character_input( $alignment_table )
	30
	31	Returns a character matrix string suitable for Phylip programs, which
	32	corresponds to the given alignment table. See Text::Tradition::Collation
	33	for a description of the alignment table format.
	34
027d819c	35	=cut
027d819c	36
9457207b	37	sub character_input {
	38	my $table = shift;
	39	my $character_matrix = _make_character_matrix( $table );
	40	my $input = '';
	41	my $rows = scalar @{$character_matrix};
	42	my $columns = scalar @{$character_matrix->[0]} - 1;
	43	$input .= "\t$rows\t$columns\n";
	44	foreach my $row ( @{$character_matrix} ) {
	45	$input .= join( '', @$row ) . "\n";
	46	}
	47	return $input;
	48	}
	49
027d819c	50	sub _make_character_matrix {
68454b71	51	my( $table ) = @_;
	52	# Push the names of the witnesses to initialize the rows of the matrix.
	53	my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] }
	54	@{$table->{'alignment'}};
	55	foreach my $token_index ( 0 .. $table->{'length'} - 1) {
	56	# First implementation: make dumb alignment table, caring about
	57	# nothing except which reading is in which position.
	58	my @pos_readings = map { $_->{'tokens'}->[$token_index] }
	59	@{$table->{'alignment'}};
	60	my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;
027d819c	61	my @chars = _convert_characters( \@pos_text );
68454b71	62	foreach my $idx ( 0 .. $#matrix ) {
	63	push( @{$matrix[$idx]}, $chars[$idx] );
	64	}
	65	}
	66	return \@matrix;
	67	}
	68
	69	# Helper function to make the witness name something legal for pars
	70
	71	sub _normalize_witname {
	72	my( $witname ) = @_;
	73	$witname =~ s/\s+/ /g;
	74	$witname =~ s/[\[\]\(\)\:;,]//g;
	75	$witname = substr( $witname, 0, 10 );
	76	return sprintf( "%-10s", $witname );
	77	}
	78
027d819c	79	sub _convert_characters {
68454b71	80	my $row = shift;
	81	# This is a simple algorithm that treats every reading as different.
	82	# Eventually we will want to be able to specify how relationships
	83	# affect the character matrix.
	84	my %unique = ( '__UNDEF__' => 'X',
	85	'#LACUNA#' => '?',
	86	);
	87	my %count;
	88	my $ctr = 0;
	89	foreach my $word ( @$row ) {
	90	if( $word && !exists $unique{$word} ) {
	91	$unique{$word} = chr( 65 + $ctr );
	92	$ctr++;
	93	}
	94	$count{$word}++ if $word;
	95	}
	96	# Try to keep variants under 8 by lacunizing any singletons.
	97	if( scalar( keys %unique ) > 8 ) {
	98	foreach my $word ( keys %count ) {
	99	if( $count{$word} == 1 ) {
	100	$unique{$word} = '?';
	101	}
	102	}
	103	}
	104	my %u = reverse %unique;
	105	if( scalar( keys %u ) > 8 ) {
	106	warn "Have more than 8 variants on this location; phylip will break";
	107	}
	108	my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
	109	return @chars;
	110	}
	111
027d819c	112	=head2 phylip_pars( $character_matrix )
	113
	114	Runs Phylip Pars on the given character matrix. Returns results in Newick format.
	115
	116	=cut
	117
b02332ca	118	sub phylip_pars {
	119	my( $charmatrix ) = @_;
	120	# Set up a temporary directory for all the default Phylip files.
	121	my $phylip_dir = File::Temp->newdir();
	122	# $phylip_dir->unlink_on_destroy(0);
	123	# We need an infile, and we need a command input file.
	124	open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
	125	print MATRIX $charmatrix;
	126	close MATRIX;
	127
	128	open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
	129	## TODO any configuration parameters we want to set here
	130	# U Search for best tree? Yes
	131	# S Search option? More thorough search
	132	# V Number of trees to save? 100
	133	# J Randomize input order of species? No. Use input order
	134	# O Outgroup root? No, use as outgroup species 1
	135	# T Use Threshold parsimony? No, use ordinary parsimony
	136	# W Sites weighted? No
	137	# M Analyze multiple data sets? No
	138	# I Input species interleaved? Yes
	139	# 0 Terminal type (IBM PC, ANSI, none)? ANSI
	140	# 1 Print out the data at start of run No
	141	# 2 Print indications of progress of run Yes
	142	# 3 Print out tree Yes
	143	# 4 Print out steps in each site No
	144	# 5 Print character at all nodes of tree No
	145	# 6 Write out trees onto tree file? Yes
	146	print CMD "Y\n";
	147	close CMD;
	148
	149	# And then we run the program.
	150	my $program = File::Which::which( 'pars' );
	151	unless( -x $program ) {
edac47cc	152	throw( "Phylip pars not found in path" );
b02332ca	153	}
	154
	155	{
	156	# We need to run it in our temporary directory where we have created
	157	# all the expected files.
	158	local $CWD = $phylip_dir;
	159	my @cmd = ( $program );
	160	run \@cmd, '<', 'cmdfile', '>', '/dev/null';
	161	}
	162	# Now our output should be in 'outfile' and our tree in 'outtree',
	163	# both in the temp directory.
	164
	165	my @outtree;
	166	if( -f "$phylip_dir/outtree" ) {
	167	open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
	168	@outtree = <TREE>;
	169	close TREE;
	170	}
edac47cc	171	return join( '', @outtree ) if @outtree;
b02332ca	172
69403daa	173	# If we got this far, we are about to throw an error.
b02332ca	174	my @error;
	175	if( -f "$phylip_dir/outfile" ) {
	176	open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
	177	@error = <OUTPUT>;
	178	close OUTPUT;
	179	} else {
	180	push( @error, "Neither outtree nor output file was produced!" );
	181	}
edac47cc	182	throw( join( '', @error ) );
b02332ca	183	}
b02332ca	184
027d819c	185	=head2 parse_newick( $newick_string )
	186
	187	Parses the given Newick tree(s) into one or more undirected Graph objects.
	188
	189	=cut
	190
b02332ca	191	sub parse_newick {
	192	my $newick = shift;
	193	my @trees;
	194	# Parse the result into a tree
	195	my $forest = Bio::Phylo::IO->parse(
	196	-format => 'newick',
	197	-string => $newick,
	198	);
	199	# Turn the tree into a graph, starting with the root node
	200	foreach my $tree ( @{$forest->get_entities} ) {
	201	push( @trees, _graph_from_bio( $tree ) );
	202	}
	203	return \@trees;
	204	}
	205
027d819c	206	=head2 newick_to_svg( $newick_string )
	207
	208	Uses the FigTree utility (if installed) to transform the given Newick tree(s)
	209	into a graph visualization.
	210
	211	=cut
	212
27e2a8fe	213	sub newick_to_svg {
	214	my $newick = shift;
	215	my $program = File::Which::which( 'figtree' );
	216	unless( -x $program ) {
edac47cc	217	throw( "FigTree commandline utility not found in path" );
27e2a8fe	218	}
	219	my $svg;
	220	my $nfile = File::Temp->new();
	221	print $nfile $newick;
	222	close $nfile;
	223	my @cmd = ( $program, '-graphic', 'SVG', $nfile );
	224	run( \@cmd, ">", binary(), \$svg );
	225	return decode_utf8( $svg );
	226	}
	227
b02332ca	228	sub _graph_from_bio {
	229	my $tree = shift;
	230	my $graph = Graph->new( 'undirected' => 1 );
	231	# Give all the intermediate anonymous nodes a name.
	232	my $i = 0;
	233	foreach my $n ( @{$tree->get_entities} ) {
	234	next if $n->get_name;
	235	$n->set_name( $i++ );
	236	}
	237	my $root = $tree->get_root->get_name;
	238	$graph->add_vertex( $root );
	239	_add_tree_children( $graph, $root, $tree->get_root->get_children() );
	240	return $graph;
	241	}
	242
	243	sub _add_tree_children {
	244	my( $graph, $parent, $tree_children ) = @_;
	245	foreach my $c ( @$tree_children ) {
	246	my $child = $c->get_name;
	247	$graph->add_vertex( $child );
	248	$graph->add_path( $parent, $child );
	249	_add_tree_children( $graph, $child, $c->get_children() );
	250	}
	251	}
edac47cc	252
	253	sub throw {
	254	Text::Tradition::Error->throw(
	255	'ident' => 'StemmaUtil error',
	256	'message' => $_[0],
	257	);
	258	}
	259
027d819c	260	1;
	261
	262	=head1 LICENSE
	263
	264	This package is free software and is provided "as is" without express
	265	or implied warranty. You can redistribute it and/or modify it under
	266	the same terms as Perl itself.
	267
	268	=head1 AUTHOR
	269
	270	Tara L Andrews E<lt>aurum@cpan.orgE<gt>