# HG changeset patch
# User Dannon Baker <dannonbaker@me.com>
# Date 1333492227 21600
# Node ID 016f6375aadc63362d4eaabaa2e88cd84b3083c8
# Parent  4f3fe44edb3f6a0821e86569f169c2a775faabfb
Initial commit of metaphlan_to_phyloxml converter.

diff -r 4f3fe44edb3f -r 016f6375aadc metaphlan_to_phyloxml.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_to_phyloxml.py	Tue Apr 03 16:30:27 2012 -0600
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+"""
+Read metaphaln output summarizing taxonomic distribution and format in PhyloXML format
+
+usage: %prog metaphlan.txt phylo.xml
+"""
+
+import sys
+
+# Metaphlan output looks like:
+#   k__Bacteria   99.07618
+#   k__Archaea  0.92382
+#   k__Bacteria|p__Proteobacteria   82.50732
+#   k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria    81.64905
+
+rank_map = { 'k__': 'kingdom', 'p__': 'phylum', 'c__': 'class', 'o__': 'order', 'f__': 'family', 'g__': 'genus', 's__': 'species' }
+
+class Node( object ):
+    """Node in a taxonomy"""
+    def __init__( self, rank=None, name=None ):
+        self.rank = rank
+        self.name = name
+        self.value = None
+        self.children = dict()
+    @staticmethod
+    def from_metaphlan_file( file ):
+        """
+        Build tree from metaphlan output
+        """
+        root = Node()
+        for line in file:
+            taxa, abundance = line.split()
+            parts = taxa.split( "|" )
+            root.add( parts, abundance )
+        return root
+    def add( self, parts, value ):
+        """
+        Parts is a list of node names, recursively add nodes until we reach
+        the last part, and then attach the value to that node.
+        """
+        if len( parts ) == 0:
+            self.value = value
+        else:
+            next_part = parts.pop(0)
+            rank = rank_map[ next_part[:3] ]
+            name = next_part[3:]
+            if name not in self.children:
+                self.children[name] = Node( rank, name )
+            self.children[name].add( parts, value )
+    def __str__( self ):
+        if self.children:   
+            return "(" + ",".join( str( child ) for child in self.children.itervalues() ) + "):" + self.name
+        else:
+            return self.name
+    def to_phyloxml( self, out ):
+        print >>out, "<clade>"
+        if self.name:
+            print >>out, "<name>%s</name>" % self.name
+            print >>out, "<taxonomy><scientific_name>%s</scientific_name><rank>%s</rank></taxonomy>" % ( self.name, self.rank )
+        if self.value:
+            print >>out, "<property datatype='xsd:float' ref='metaphlan:abundance' applies_to='node'>%s</property>" % self.value
+            ## print >>out, "<confidence type='abundance'>%s</confidence>" % self.value
+        for child in self.children.itervalues():
+            child.to_phyloxml( out )
+        print >>out, "</clade>"
+
+out = open( sys.argv[2], 'w' )
+
+print >>out, '<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">'
+print >>out, '<phylogeny rooted="true">'
+
+Node.from_metaphlan_file( open( sys.argv[1] ) ).to_phyloxml( out )
+
+print >>out, '</phylogeny>'
+print >>out, '</phyloxml>'
diff -r 4f3fe44edb3f -r 016f6375aadc metaphlan_to_phyloxml.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_to_phyloxml.xml	Tue Apr 03 16:30:27 2012 -0600
@@ -0,0 +1,17 @@
+<tool id="meta_to_phylo" name="MetaPhlAn to PhyloXML" version="1.0.0">
+ <description>Converter</description>
+ <command interpreter="python">
+metaphlan_to_phyloxml.py $input $output
+ </command>
+ <inputs>
+  <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
+ </inputs>
+ <outputs>
+    <data format="xml" name="output" label="${tool.name} on ${on_string}" /> 
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  MetaPhlAn to PhyloXML Converter
+ </help>
+</tool>