Mercurial > repos > dannon > metaphlan

annotate metaphlan_to_phyloxml.py @ 5:73f082e9fa2d

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Set of improvements and fixes from Nicola Soranzo changeset: 9:c3dae016a3eb files: metaphlan.xml description: Update citation changeset: 8:f58b66b4e5fc files: metaphlan.xml description: Add select lists for -t and --tax_lev options Also some small fixes changeset: 7:94a2b29778b7 files: metaphlan_to_phyloxml.xml description: Clarify that only result of rel_ab analysis is accepted as input changeset: 6:b0eba028dee8 files: metaphlan.xml metaphlan_to_phyloxml.xml description: Fix whitespaces changeset: 5:4340075c8a93 files: tool_dependencies.xml description: Correct metaphlan clone URL to avoid a redirect changed metaphlan.xml changed metaphlan_to_phyloxml.xml changed tool_dependencies.xml
author nsegata
date Sun, 23 Dec 2012 18:46:23 +0100
parents 016f6375aadc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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1 #!/usr/bin/env python
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2
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3 """
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4 Read metaphaln output summarizing taxonomic distribution and format in PhyloXML format
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5
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6 usage: %prog metaphlan.txt phylo.xml
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7 """
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8
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9 import sys
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10
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11 # Metaphlan output looks like:
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12 # k__Bacteria 99.07618
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13 # k__Archaea 0.92382
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14 # k__Bacteria|p__Proteobacteria 82.50732
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15 # k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 81.64905
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16
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17 rank_map = { 'k__': 'kingdom', 'p__': 'phylum', 'c__': 'class', 'o__': 'order', 'f__': 'family', 'g__': 'genus', 's__': 'species' }
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18
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19 class Node( object ):
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20 """Node in a taxonomy"""
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21 def __init__( self, rank=None, name=None ):
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22 self.rank = rank
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23 self.name = name
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24 self.value = None
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25 self.children = dict()
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26 @staticmethod
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27 def from_metaphlan_file( file ):
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28 """
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29 Build tree from metaphlan output
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30 """
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31 root = Node()
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32 for line in file:
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33 taxa, abundance = line.split()
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34 parts = taxa.split( "|" )
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35 root.add( parts, abundance )
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36 return root
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37 def add( self, parts, value ):
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38 """
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39 Parts is a list of node names, recursively add nodes until we reach
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40 the last part, and then attach the value to that node.
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41 """
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42 if len( parts ) == 0:
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43 self.value = value
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44 else:
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45 next_part = parts.pop(0)
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46 rank = rank_map[ next_part[:3] ]
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47 name = next_part[3:]
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48 if name not in self.children:
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49 self.children[name] = Node( rank, name )
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50 self.children[name].add( parts, value )
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51 def __str__( self ):
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52 if self.children:
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53 return "(" + ",".join( str( child ) for child in self.children.itervalues() ) + "):" + self.name
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54 else:
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55 return self.name
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56 def to_phyloxml( self, out ):
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57 print >>out, "<clade>"
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58 if self.name:
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59 print >>out, "<name>%s</name>" % self.name
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60 print >>out, "<taxonomy><scientific_name>%s</scientific_name><rank>%s</rank></taxonomy>" % ( self.name, self.rank )
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61 if self.value:
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62 print >>out, "<property datatype='xsd:float' ref='metaphlan:abundance' applies_to='node'>%s</property>" % self.value
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63 ## print >>out, "<confidence type='abundance'>%s</confidence>" % self.value
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64 for child in self.children.itervalues():
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65 child.to_phyloxml( out )
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66 print >>out, "</clade>"
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67
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68 out = open( sys.argv[2], 'w' )
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69
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70 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">'
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71 print >>out, '<phylogeny rooted="true">'
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72
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73 Node.from_metaphlan_file( open( sys.argv[1] ) ).to_phyloxml( out )
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74
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75 print >>out, '</phylogeny>'
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76 print >>out, '</phyloxml>'