Bluesky's blog
newick 格式和phyloxml格式是遗传发育树的两种最为常见的格式，所以它们两者的互转非常重要。
首先讲讲两种文件的特点：
newick: http://evolution.genetics.washington.edu/phylip/newicktree.html
phyloxml: http://www.phyloxml.org
两者除了格式上一个采用括号，一个采用XML标签的差别外，主要是newick一般包含的信息比较少，只有id和branch length, 而phyloxml 包含的信息相当丰富，包括 scientific name, name, gene accession, sequence, 等等，一切能想到到的信息都可以通过拓展phyloxml schema来实现（详情可phyloxml的说明）。
newick转phyloxml我这里提供2种方式：
1. forester decorater: https://sites.google.com/site/cmzmasek/home/software/forester/decorator (可能被屏蔽，若不能访问得翻墙)
因为newick包含的信息少于phyloxml的信息，所以最重的就是根据newick的ID通过其他方式提取到其他你需要添加到phyloxml的信息，并按decorater说明各项以Tab键分隔。下面的这个程序就是从uniport下载的specieslist.txt中提取信息输出为一个以Tab分隔的信息文件。
#! /usr/bin/perl
use strict;
use warnings;
open IN,"<","$ARGV[0]"; open OUT,">","$ARGV[1]";
open IN2,"<","/Users/yangl/Documents/test/specieslist.txt";
my %sci_name;
my %tax_id;
while(){
#ALCCR E 85095: N=Alcedo cristata
chomp;
if(/(\w+)\s+\w+\s+(\d+):\s+N=(.+)$/){
$tax_id{$1}=$2;
$sci_name{$1}=$3;
}
}
while(){
my @name = split/:/,$_;
foreach my $name(@name){
if ($name=~/[\(|\)|,]([A-Z]+.*)$/){
my $accession = $1;
# print $accession . "\n";
if ($1=~/(.+)_(\w+)/){
#print OUT "$accession\tTAXONOMY_CODE:$2\tTAXONOMY_ID:$tax_id{$2}\tTAXONOMY_SN:$sci_name{$2}\tSEQ_ACCESSION:$1\tSEQ_ACCESSION_SOURCE:ncbi\tSEQ_NAME:$1\n";
print OUT "$accession\t";
#print "$2\n";
print OUT "TAXONOMY_SN:$sci_name{$2}\t";
print OUT "SEQ_ACCESSION:$1\t";
print OUT "SEQ_ACCESSION_SOURCE:ncbi\t";
print OUT "SEQ_NAME:$1\n";
}
}
}
}
2.perl 包： Bio::TreeIO::phyloxml (利用perl包可进行newick和phyloxml格式的互转)，程序示例如下：
#! /usr/bin/perl
use strict;
use warnings;
use Bio::TreeIO;
use Data::Dumper;
###
#注意: "Bio::TreeIO 的write_tree重新生成的树文件格式需要重排" -已修改Pm文件
###
open OUT,">","name_accession_sciname.txt";
my $treeio = Bio::TreeIO->new(-format => 'phyloxml',
-file => '/Users/yangl/Documents/test/wnt_gene_tree.xml');
my $tree = $treeio->next_tree;
my $newfile="newfile.newick";
#print Dumper($treeio);
my @nodes = $tree->get_nodes();
my @not_leaf_nodes;
#print scalar @nodes;
foreach my $node (@nodes){
if($node->is_Leaf){
my ($sci_name) = $treeio -> read_annotation('-obj'=>$node, '-path'=>'taxonomy/scientific_name',-attr=>0);
my $accession = $node -> {"_sequence"}[0] -> {"_annotation"} -> {"_annotation"} -> {"accession"}[0] -> {"_annotation"} -> {"_text"}[0] -> {"value"};
#print $accession . "\n";
my $seq_name = $node -> {"_sequence"}[0] -> {"_annotation"} -> {"_annotation"} -> {"name"}[0] -> {"_annotation"} -> {"_text"}[0] -> {"value"};
my $acc = $accession;
$acc=~s/\s/\-/g;
$node->id($acc);
print OUT "$acc\tTAXONOMY_SN:$sci_name\tSEQ_ACCESSION_SOURCE:ncbi\tSEQ_ACCESSION:$accession\tSEQ_NAME:$seq_name\n";
#$node = $treeio->add_phyloXML_annotation(-obj=>$node,-attr=>"name = $accession");
$node -> add_tag_value("name",$sci_name);
}else{
#push @not_leaf_nodes,$node;
}
}
my $treeout = Bio::TreeIO->new (-format => 'phyloxml',-file=>"> newfile2.xml");
$treeout->write_tree($tree); #phyloxml转phyloxml（修改phyloxml的信息后重新生成phyloxml文件，如修改scitific name）,其实newick转phyloxml也一样，只是需要添加你想要的其他信息而不是修改信息
#my $treeout = Bio::TreeIO->new (-format => 'newick',-file=>"> newfile_newick.xml");
#$treeout->write_tree($tree) #phyloxml转newick
注意：利用phyloxml包转换成phyloxml，会导致以下问题：1.失去缩进，整个文件变成一行； 2.各XML标签的顺序会随机出现
1. 失去缩进：没有修改程序所进，但可以通过将模式 ” >< ” 替换成 ” >\n< ” ，来换行显示
2. 已经修改 AnnotatableNode.pm 和 phyloxml.pm 使得我们能自定义标签顺序。
a. 在 AnnotatableNode.pm 倒数第二行（” 1；” 这一行之前）加入自定义排序函数：
=head2 _ann_sort (written by yangli)
Title : _ann_sort
Usage : @ann = $tree->($order, @ann)
Function: Rearrange Annotation to requested order.
Returns : An array of annotation tag in requested order.
Args : An array of annotationI.
=cut
sub _ann_sort
{
my ($self, $order,@ann) = @_;
my @ordered;
my @order_index;
my %ann;
my @other;
foreach my $ann(@ann){
my $key = $ann->tagname;
$ann{$key}=$ann;
}
foreach my $order_key (@$order){
foreach my $key (keys %ann){
if ($key eq $order_key){
push @ordered,$ann{$key};
delete $ann{$key};
}
}
}
@other = values %ann;
return (@ordered,@other);
}
b.在phyloxml.pm对应位置调用。
在print_annotation函数中调用自定义函数_ann_sort()：
=head2 print_annotation
Title : print_annotation
Usage : $str = $annotatablenode->print_annotation($str, $annotationcollection)
Function: prints the annotationCollection in a phyloXML format.
Returns : string of annotation information
Args : string to which the Annotation should be concatenated to,
annotationCollection that holds the Annotations
=cut
# Again, it may be more appropriate to make a separate Annotation::phyloXML object
# and have this subroutine within that object so it can handle the
# reading and writing of the values and attributes.
# especially since this function is used both by
# Bio::TreeIO::phyloxml (through write_tree) and
# Bio::Node::AnnotatableNode (through node_to_string).
# but since tagTree is a temporary stub and I didn't want to make
# a redundant object I've put it here for now.
sub print_annotation
{
my ($self, $str, $ac) = @_;
my @all_anns = $ac->get_Annotations();
#print blessed($self);
#调用自定义_ann_sorted函数，规定顺序依次是name branch_length taxonomy,若还存在其他标签其他标签顺序随机
my @all_anns_sorted = $self->_ann_sort([qw(name branch_length taxonomy)],@all_anns);
foreach my $ann (@all_anns_sorted) {
my $key = $ann->tagname;
if ($key eq '_attr') { next; } # attributes are already printed in the previous level
if ($ann->isa('Bio::Annotation::SimpleValue'))
{
if ($key eq '_text') {
$str .= $ann->value;
}
else {
$str .= "<$key>";
$str .= $ann->value;
$str .= "";
}
}
elsif ($ann->isa('Bio::Annotation::Collection'))
{
my @attrs = $ann->get_Annotations('_attr');
if (@attrs) { # if there is a attribute collection
$str .= "<$key"; $str = print_attr($self, $str, $attrs[0]); $str .= ">";
}
else {
$str .= "<$key>";
}
$str = print_annotation($self, $str, $ann);
$str .= "";
}
}
return $str;
}
在print_seq_annotation函数中调用自定义函数_ann_sort()：
=head2 print_sequence_annotation
Title : print_sequence_annotation
Usage : $str = $node->print_seq_annotation( $str, $seq );
Function: prints the Bio::Seq object associated with the node
in a phyloXML format.
Returns : string that describes the sequence
Args : string to which the Annotation should be concatenated to,
Seq object to print in phyloXML
=cut
# Again, it may be more appropriate to make a separate Annotation::phyloXML object
# and have this subroutine within that object so it can handle the
# reading and writing of the values and attributes.
# especially since this function is used both by
# Bio::TreeIO::phyloxml (through write_tree) and
# Bio::Node::AnnotatableNode (through node_to_string).
# but since tagTree is a temporary stub and I didn't want to make
# a redundant object I've put it here for now.
sub print_seq_annotation
{
my ($self, $str, $seq) = @_;
$str .= "annotation->get_Annotations('_attr'); # check id_source
if ($attr) {
my ($id_source) = $attr->get_Annotations('id_source');
if ($id_source) {
$str .= " id_source=\"".$id_source->value."\"";
}
}
$str .= ">";
my @all_anns = $seq->annotation->get_Annotations();
#调用排序子程序_ann_sort(),若有accession和name,先排accession然后name，再排其他标签。
my @all_anns_sorted = $self->_ann_sort([qw(accession name)],@all_anns);
foreach my $ann (@all_anns_sorted) {
my $key = $ann->tagname;
if ($key eq '_attr') { next; } # attributes are already printed in the previous level
if ($ann->isa('Bio::Annotation::SimpleValue'))
{
if ($key eq '_text') {
$str .= $ann->value;
}
else {
$str .= "<$key>";
$str .= $ann->value;
$str .= "";
}
}
elsif ($ann->isa('Bio::Annotation::Collection'))
{
my @attrs = $ann->get_Annotations('_attr');
if (@attrs) { # if there is a attribute collection
$str .= "<$key";
$str = print_attr($self, $str, $attrs[0]);
$str .= ">";
}
else {
$str .= "<$key>";
}
$str = print_annotation($self, $str, $ann);
$str .= "";
}
}
# print mol_seq
if ($seq->seq()) {
$str .= "";
$str .= $seq->seq();
$str .= " ";
}
$str .= "";
return $str;
}
修改以后就能使XML标签按你自己的顺序排序,修改后的.pm文件下载地址：链接http://pan.baidu.com/s/1bndh9D1 密码: xbe6，对应覆盖Perl/5.18/Bio/Tree目录中的AnnotatableNode.pm和Perl/5.18/Bio/TreeIO目录中的phyloxml.pm即可。
尊重他人劳动成果，转载请注明出处:Bluesky's blog » newick转phyloxml
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