itis_taxonomy.py

import urllib2
import Bio.Phylo as bp
from Bio.Phylo import Newick
import os
import tarfile


col_delimiter = '|'
url = 'http://www.itis.gov/downloads/itisMySQLTables.tar.gz'
tree_filename = 'itis_taxonomy.newick'
tree_format = 'newick'
data_dir = 'data/'

if not os.path.exists(data_dir): os.mkdir(data_dir)

# download the taxonomy archive
filename = os.path.join(data_dir, url.split('/')[-1])
if os.path.exists(filename):
    print 'Using existing copy of %s' % filename
else:
    print 'Downloading %s...' % filename
    r = urllib2.urlopen(urllib2.Request(url))
    assert r.geturl() == url
    with open(filename, 'wb') as output_file:
        output_file.write(r.read())
    r.close()

# extract the tables
for extract in ('taxonomic_units', 'longnames'):
    if os.path.exists(os.path.join(data_dir, extract)):
        print 'Using existing copy of %s' % extract
    else:
        print 'Extracting %s from %s...' % (extract, filename)
        archive = tarfile.open(name=filename, mode='r:gz')
        full_extract = [x for x in archive.getnames() if x.split('/')[-1] == extract][0]
        member = archive.getmember(full_extract)
        member.name = extract
        archive.extract(extract, path=data_dir)
        archive.close()

# get names for all ITIS TSNs from longnames table
print 'Getting names...'
names = {}
with open(os.path.join(data_dir, 'longnames')) as names_file:
    for line in names_file:
        line = line.strip()
        values = line.split(col_delimiter)
        tax_id, name = values
        names[tax_id] = name

# read all node info from taxonomic_units
print 'Reading taxonomy...'
nodes = {}
with open(os.path.join(data_dir, 'taxonomic_units')) as nodes_file:
    for line in nodes_file:
        line = line.strip()
        values = line.split(col_delimiter)
        
        (tax_id, usage, parent_id,
            uncertain_parent) = [values[n] for n in (0, 10, 17, 23)]
        
        #if uncertain_parent: continue
        if not usage in ('accepted', 'valid'): continue
        
        name = names[tax_id]
        this_node = Newick.Clade(name=name)
        nodes[tax_id] = this_node
        this_node.parent = parent_id
        
nodes['0'] = root_node = Newick.Clade()

# create tree from nodes dictionary
print 'Building tree...'
for node_id, this_node in nodes.iteritems():
    if node_id == '0': continue
    
    try:
        parent_node = nodes[this_node.parent]
        parent_node.clades.append(this_node)

    except KeyError: pass
    
    del this_node.parent

tree = Newick.Tree(root=root_node)

# write tree to file
print 'Writing %s tree to %s...' % (tree_format, tree_filename)
bp.write([tree], tree_filename, tree_format)

print 'Done!'''