示例#1
0
#!/usr/bin/env python
import sys
import os
from treestore import Treestore


try: taxonomy = sys.argv[1]
except: taxonomy = None

t = Treestore()

treebase_uri = 'http://purl.org/phylo/treebase/phylows/tree/%s'

tree_files = [x for x in os.listdir('trees') if x.endswith('.nex')]
base_uri = 'http://www.phylocommons.org/trees/%s'
tree_list = set(t.list_trees())
for tree_uri in tree_list:
    if not 'TB2_' in tree_uri: continue
    tree_id = t.id_from_uri(tree_uri)
    tb_uri = treebase_uri % (tree_id.replace('_', ':'))
    print tree_id, tb_uri
    t.annotate(tree_uri, annotations='?tree bibo:cites <%s> .' % tb_uri)
示例#2
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from treestore import Treestore
import Bio.Phylo as bp
import time
import datetime
from cStringIO import StringIO
import sys
import cPickle as pkl

t = Treestore()
sizes = [10, 50, 100, 200, 500, 1000, 2000, 5000]
ti = lambda x: str(datetime.timedelta(seconds=round(x, 3)))[:-3]

add_times = {}
retrieve_times = {}
write_times = {}
parse_times = {}

print 'size\tadd\tretrieve\twrite\tparse'
for n in sizes:
    s = str(n).zfill(4)

    print s,
    sys.stdout.flush()
    
    start_time = time.time()
    t.add_trees('tests/bird%s.new' % s, 'newick', 'test%s' % s)
    add_times[n] = time.time() - start_time
    print '\t', ti(add_times[n]),
    sys.stdout.flush()

    start_time = time.time()
示例#3
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def uri_from_tree_id(tree_id):
    return Treestore.uri_from_id(tree_id, base_uri=settings.TREE_URI)
示例#4
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#!/usr/bin/env python
import sys
import os
from treestore import Treestore


try: taxonomy = sys.argv[1]
except: taxonomy = None

t = Treestore()

tree_files = [x for x in os.listdir('trees') if x.endswith('.nex')]
base_uri = 'http://www.phylocommons.org/trees/%s'
tree_list = set(t.list_trees())
if taxonomy:
    sys.stdout.write('Loading taxonomy...')
    sys.stdout.flush()
    taxonomy = t.get_trees('%s_taxonomy' % taxonomy)[0]
    taxonomy.index_labels()
    print 'done.'

errors = set()
for tree_file in tree_files:
    tree_id = 'TB2_' + tree_file[:-len('.nex')]
    if Treestore.uri_from_id(tree_id) in tree_list: continue
    print '**', tree_id
    tree_path = os.path.join('trees', tree_file)
    with open(tree_path) as input_file:
        r = input_file.read()
    if '<!DOCTYPE html' in r: continue
    try:
示例#5
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def tree_id_from_uri(uri):
    return Treestore.id_from_uri(uri, base_uri=settings.TREE_URI)