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test_assign_taxonomy.py
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test_assign_taxonomy.py
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#!/usr/bin/env python
"""Tests of code for assigning taxonomy"""
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2010, The QIIME Project"
#remember to add yourself if you make changes
__credits__ = ["Greg Caporaso", "Kyle Bittinger"]
__license__ = "GPL"
__version__ = "0.92"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from cStringIO import StringIO
from os import remove, system
from glob import glob
from tempfile import NamedTemporaryFile
from shutil import copy as copy_file
from cogent.util.unit_test import TestCase, main
from cogent import LoadSeqs
from cogent.app.util import get_tmp_filename
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.util.misc import remove_files
from cogent.parse.fasta import MinimalFastaParser
from qiime.assign_taxonomy import TaxonAssigner, BlastTaxonAssigner,\
RdpTaxonAssigner
class TaxonAssignerTests(TestCase):
"""Tests of the abstract TaxonAssigner class"""
def test_init(self):
"""Abstract TaxonAssigner __init__ should store name, params"""
p = TaxonAssigner({})
self.assertEqual(p.Name, 'TaxonAssigner')
self.assertEqual(p.Params, {})
def test_call(self):
"""Abstract TaxonAssigner __call__ should raise NotImplementedError"""
p = TaxonAssigner({})
self.assertRaises(NotImplementedError, p, '/path/to/seqs')
class BlastTaxonAssignerTests(TestCase):
"""Tests of the BlastTaxonAssigner class"""
def setUp(self):
self.id_to_taxonomy_fp = get_tmp_filename(\
prefix='BlastTaxonAssignerTests_',suffix='.txt')
self.input_seqs_fp = get_tmp_filename(\
prefix='BlastTaxonAssignerTests_',suffix='.fasta')
self.reference_seqs_fp = get_tmp_filename(\
prefix='BlastTaxonAssignerTests_',suffix='.fasta')
self._paths_to_clean_up =\
[self.id_to_taxonomy_fp,self.input_seqs_fp,self.reference_seqs_fp]
open(self.id_to_taxonomy_fp,'w').write(id_to_taxonomy_string)
open(self.input_seqs_fp,'w').write(test_seq_coll.toFasta())
self.test_seqs = test_seq_coll.items()
open(self.reference_seqs_fp,'w').write(test_refseq_coll.toFasta())
self.expected1 = {
's1': ('Archaea;Euryarchaeota;Halobacteriales;uncultured', 0.0),
's2': ('Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.', 0.0),
's3': ('Archaea;Crenarchaeota;uncultured;uncultured', 0.0),
's4': ('Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium', 0.0),
's5': ('Archaea;Crenarchaeota;uncultured;uncultured', 0.0),
's6': ('No blast hit', None),
}
def tearDown(self):
remove_files(set(self._paths_to_clean_up))
def test_init(self):
"""BlastTaxonAssigner __init__ should store name, params"""
p = BlastTaxonAssigner({})
self.assertEqual(p.Name, 'BlastTaxonAssigner')
# default parameters correctly initialized
default_params = {'Min percent identity':0.90,\
'Max E value':1e-30,\
'Application':'blastn/megablast'}
self.assertEqual(p.Params, default_params)
def test_parse_id_to_taxonomy_file(self):
"""Parsing taxonomy files functions as expected
"""
lines = id_to_taxonomy_string.splitlines()
p = BlastTaxonAssigner({})
expected = {\
"AY800210":"Archaea;Euryarchaeota;Halobacteriales;uncultured",\
"EU883771":"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",\
"EF503699":"Archaea;Crenarchaeota;uncultured;uncultured",\
"DQ260310":"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",\
"EF503697":"Archaea;Crenarchaeota;uncultured;uncultured"}
self.assertEqual(p._parse_id_to_taxonomy_file(lines),expected)
def test_map_ids_to_taxonomy(self):
"""Mapping sequence ids to taxonomy functions as expected
"""
p = BlastTaxonAssigner({})
id_to_taxonomy_map = {
"AY800210": "Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771": "Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": "Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310": "Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": "Archaea;Crenarchaeota;uncultured;uncultured",
}
hits = {
's1': ("AY800210", 1e-99),
's5': ("EU883771", 'weird confidence value'),
's3': ("DQ260310", 42.),
's4': None,
}
expected = {
's1': ("Archaea;Euryarchaeota;Halobacteriales;uncultured", 1e-99),
's5': ('Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.',
'weird confidence value'),
's3': ("Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium", 42.),
's4': ('No blast hit', None),
}
actual = p._map_ids_to_taxonomy(hits,id_to_taxonomy_map)
self.assertEqual(actual,expected)
def test_get_first_blast_hit_per_seq(self):
"""Extracting the first blast hit for each seq functions as expected
"""
p = BlastTaxonAssigner({})
blast_hits = {'s1':[('blah',0.0)],\
's3':[('dsasd',1e-42),('rrr',1e-12),('qqq',0.001)],\
's2':[]}
expected = {'s1':('blah',0.0),\
's3':('dsasd',1e-42),\
's2':None}
actual = p._get_first_blast_hit_per_seq(blast_hits)
self.assertEqual(actual,expected)
def test_get_blast_hits(self):
"""BlastTaxonAssigner._get_blast_hits functions w existing db
"""
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({})
seq_coll_blast_results = p._get_blast_hits(blast_db,self.test_seqs)
# mapping from identifier in test_seq_coll to the id of the sequence
# in the refseq collection (a silva derivative)
expected_matches = {\
's1':'AY800210',
's2':'EU883771',\
's3':'EF503699',\
's4':'DQ260310',\
's5':'EF503697'}
# no results for s6 (which is a randomly-generated sequence)
s6_blast_results = seq_coll_blast_results['s6']
self.assertEqual(s6_blast_results,[])
# expected results for all other query sequences
for seq_id in expected_matches:
blast_results = seq_coll_blast_results[seq_id]
blast_results_d = dict(blast_results)
# explicitly checks that the result is in the data before
# pulling it out (this is redundant, but allows for a useful
# error message if the data wasn't in there b/c e.g. there
# were no blast results returned)
self.assertTrue(expected_matches[seq_id] in blast_results_d)
# now check that the perfect match got a 0.0 e-value as it should
# on this data
self.assertEqual(blast_results_d[expected_matches[seq_id]],0.0)
def test_call_existing_blast_db(self):
"""BlastTaxonAssigner.__call__ functions w existing db
"""
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({'blast_db':blast_db,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
actual = p(self.input_seqs_fp)
self.assertEqual(actual,self.expected1)
def test_call_alt_input_types(self):
"""BlastTaxonAssigner.__call__ functions w alt input types """
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
# neither seqs or seq_fp passed results in AssertionError
self.assertRaises(AssertionError,p)
# Functions with a list of (seq_id, seq) pairs
seqs = list(MinimalFastaParser(open(self.input_seqs_fp)))
actual = p(seqs=seqs)
self.assertEqual(actual,self.expected1)
# Functions with input path
actual = p(self.input_seqs_fp)
self.assertEqual(actual,self.expected1)
# same result when passing fp or seqs
self.assertEqual(p(seqs=seqs),p(self.input_seqs_fp))
def test_seqs_to_taxonomy(self):
"""BlastTaxonAssigner._seqs_to_taxonomy: functions as expected
"""
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
# build the id_to_taxonomy_map as this test doesn't execute __call__
id_to_taxonomy_map = {
"AY800210": \
"Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771": \
"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": \
"Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310": \
"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": \
"Archaea;Crenarchaeota;uncultured;uncultured",
}
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
# read the input file into (seq_id, seq) pairs
seqs = list(MinimalFastaParser(open(self.input_seqs_fp)))
actual = p._seqs_to_taxonomy(seqs,blast_db,id_to_taxonomy_map)
self.assertEqual(actual,self.expected1)
# passing empty list of seqs functions as expected
actual = p._seqs_to_taxonomy([],blast_db,id_to_taxonomy_map)
self.assertEqual(actual,{})
def test_call_on_the_fly_blast_db(self):
"""BlastTaxonAssigner.__call__ functions w creating blast db
"""
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
actual = p(self.input_seqs_fp)
self.assertEqual(actual,self.expected1)
def test_call_output_to_file(self):
"""BlastTaxonAssigner.__call__ functions w output to file
"""
result_path = get_tmp_filename(
prefix='BlastTaxonAssignerTests_', suffix='.fasta')
self._paths_to_clean_up.append(result_path)
p = BlastTaxonAssigner({
'reference_seqs_filepath': self.reference_seqs_fp,
'id_to_taxonomy_filepath': self.id_to_taxonomy_fp,
})
actual = p(self.input_seqs_fp, result_path=result_path)
expected_lines = set([
's1\tArchaea;Euryarchaeota;Halobacteriales;uncultured\t0.0\n',
's2\tArchaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.\t0.0\n',
's3\tArchaea;Crenarchaeota;uncultured;uncultured\t0.0\n',
's4\tArchaea;Euryarchaeota;Methanobacteriales;Methanobacterium\t0.0\n',
's5\tArchaea;Crenarchaeota;uncultured;uncultured\t0.0\n',
's6\tNo blast hit\tNone\n',
])
f = open(result_path)
observed_lines = set(f.readlines())
f.close()
self.assertEqual(observed_lines, expected_lines)
# Return value is None when result_path is provided (Not sure
# if this is what we want yet, or if we would want both so
# results could be logged to file...)
self.assertEqual(actual, None)
def test_call_logs_run(self):
"""BlastTaxonAssigner.__call__ logs the run when expected
"""
log_path = get_tmp_filename(\
prefix='BlastTaxonAssignerTests_',suffix='.fasta')
self._paths_to_clean_up.append(log_path)
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp,\
'blast_db':blast_db})
actual = p(self.input_seqs_fp,log_path=log_path)
log_file = open(log_path)
log_file_str = log_file.read()
log_file.close()
log_file_exp = [
"BlastTaxonAssigner parameters:",
'Min percent identity:0.9',
'Application:blastn/megablast',
'Max E value:1e-30',
'Result path: None, returned as dict.',
'blast_db:%s' % str(self.reference_seqs_fp)[1:-1],
'id_to_taxonomy_filepath:%s' % self.id_to_taxonomy_fp,
'Number of sequences inspected: 6',
'Number with no blast hits: 1',
'',
]
# compare data in log file to fake expected log file
# NOTE: Since p.params is a dict, the order of lines is not
# guaranteed, so testing is performed to make sure that
# the equal unordered lists of lines is present in actual and expected
self.assertEqualItems(log_file_str.split('\n'), log_file_exp)
class RdpTaxonAssignerTests(TestCase):
"""Tests for the Rdp-based taxonomy assigner.
Slow tests are a bug, and currently these tests take about 38s on
a Dual 2.3GHz Mac. Presumably most of the time is spent
initializing the Java VM on each run. If so, this problem should
be fixed upstream in PyCogent.
"""
def setUp(self):
# Temporary input file
self.tmp_seq_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTest_',
suffix='.fasta'
)
seq_file = open(self.tmp_seq_filepath, 'w')
seq_file.write(rdp_test1_fasta)
seq_file.close()
# Temporary results filename
self.tmp_res_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTestResult_',
suffix='.tsv',
)
# touch the file so we don't get an error trying to close it
open(self.tmp_res_filepath,'w').close()
# Temporary log filename
self.tmp_log_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTestLog_',
suffix='.txt',
)
# touch the file so we don't get an error trying to close it
open(self.tmp_log_filepath,'w').close()
self._paths_to_clean_up = \
[self.tmp_seq_filepath, self.tmp_res_filepath, self.tmp_log_filepath]
self.id_to_taxonomy_file = NamedTemporaryFile(
prefix='RdpTaxonAssignerTest_', suffix='.txt')
self.id_to_taxonomy_file.write(rdp_id_to_taxonomy)
self.id_to_taxonomy_file.seek(0)
self.reference_seqs_file = NamedTemporaryFile(
prefix='RdpTaxonAssignerTest_', suffix='.fasta')
self.reference_seqs_file.write(rdp_reference_seqs)
self.reference_seqs_file.seek(0)
self.default_app = RdpTaxonAssigner({})
# Why is this giving weird results (strings get increasingly longer)
# print str(self.default_app)
def tearDown(self):
remove_files(self._paths_to_clean_up)
def test_init(self):
"""RdpTaxonAssigner.__init__ should set default attributes and params
"""
a = RdpTaxonAssigner({})
self.assertEqual(a.Name, 'RdpTaxonAssigner')
def test_train_on_the_fly(self):
"""Training on-the-fly classifies reference sequence correctly with 100% certainty
"""
input_seqs_file = NamedTemporaryFile(
prefix='RdpTaxonAssignerTest_', suffix='.fasta')
input_seqs_file.write(test_seq_coll.toFasta())
input_seqs_file.seek(0)
expected = rdp_trained_test1_expected_dict
app = RdpTaxonAssigner({
'id_to_taxonomy_fp': self.id_to_taxonomy_file.name,
'reference_sequences_fp': self.reference_seqs_file.name,
})
actual = app(self.tmp_seq_filepath)
key = 'X67228 some description'
self.assertEqual(actual[key], expected[key])
def test_parse_lineage(self):
"""Lineage in csv format is correctly parsed to a list
"""
str = 'Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.;a;b'
actual = RdpTaxonAssigner._parse_lineage(str)
expected = ['Archaea', 'Euryarchaeota', 'Methanomicrobiales',
'Methanomicrobium et rel.', 'a', 'b']
self.assertEqual(actual, expected)
def test_build_tree(self):
"""RdpTaxonAssigner._build_tree() should return a tree with correct Rdp-format taxonomy
"""
tree = RdpTaxonAssigner._build_tree(self.id_to_taxonomy_file)
actual = tree.rdp_taxonomy()
# The order of the lines in this file depends on python's
# dict() implementation, so we should ideally build two sets
# of lines and check that their contents match.
expected = rdp_expected_taxonomy
self.assertEqual(actual, expected)
def test_generate_training_seqs(self):
seqs = RdpTaxonAssigner._generate_training_seqs(
self.reference_seqs_file, self.id_to_taxonomy_file)
actual = LoadSeqs(data=seqs, aligned=False).toFasta()
self.assertEqual(actual, rdp_expected_training_seqs)
def test_generate_training_files(self):
app = RdpTaxonAssigner({
'id_to_taxonomy_fp': self.id_to_taxonomy_file.name,
'reference_sequences_fp': self.reference_seqs_file.name,
})
actual_taxonomy_file, actual_training_seqs_file = \
app._generate_training_files()
# see note in test_build_tree()
self.assertEqual(actual_taxonomy_file.read(), rdp_expected_taxonomy)
def test_call_result_as_dict(self):
"""RdpTaxonAssigner should return correct taxonomic assignment
This test may periodically fail, but should be rare.
"""
expected = rdp_test1_expected_dict
min_confidence = self.default_app.Params['Confidence']
# Since there is some variation in the assignments, run
# 10 trials and make sure we get the expected result at least once
num_trials = 10
num_seqs = len(expected)
seq_ids = expected.keys()
assignment_comp_results = [False] * num_seqs
expected_assignment_comp_results = [True] * num_seqs
for i in range(num_trials):
actual = self.default_app(self.tmp_seq_filepath)
# seq ids are the same, and all input sequences get a result
self.assertEqual(actual.keys(),expected.keys())
for j,seq_id in enumerate(seq_ids):
# confidence is above threshold
self.assertTrue(actual[seq_id][1] >= min_confidence)
# confidence roughly matches expected
self.assertFloatEqual(\
actual[seq_id][1],expected[seq_id][1],0.1)
# check if the assignment is correct -- this must happen
# at least once per seq_id for the test to pass
if actual[seq_id][0] == expected[seq_id][0]:
assignment_comp_results[j] = True
if assignment_comp_results == expected_assignment_comp_results:
# break once we've seen a correct assignment for each seq
break
self.assertEqual(\
assignment_comp_results,\
expected_assignment_comp_results,\
"Taxonomic assignments never correct in %d trials." % num_trials)
def test_call_result_to_file(self):
"""RdpTaxonAssigner should save results to file
This test may periodically fail, but should be rare.
"""
expected_lines = rdp_test1_expected_lines
# Since there is some variation in the assignments, run
# 10 trials and make sure we get the expected result at least once
# for each sequence
num_trials = 10
num_seqs = len(expected_lines)
assignment_comp_results = [False] * num_seqs
expected_assignment_comp_results = [True] * num_seqs
for i in range(num_trials):
retval = self.default_app(
seq_path=self.tmp_seq_filepath,
result_path=self.tmp_res_filepath,
log_path=None)
actual = [l.strip() for l in open(self.tmp_res_filepath, 'r')]
message = "Expected return value of None but observed %s" % retval
self.assertTrue(retval is None, message)
for j in range(num_seqs):
a = actual[j]
e = expected_lines[j]
# note we're testing using startswith here to allow
# for some variability in confidence
if a.startswith(e):
assignment_comp_results[j] = True
if assignment_comp_results == expected_assignment_comp_results:
break
self.assertEqual(\
assignment_comp_results,\
expected_assignment_comp_results,\
"Taxonomic assignments never correct in %d trials." % num_trials)
def test_log(self):
"""RdpTaxonAssigner should write correct message to log file"""
# expected result when no result_path is provided
a = RdpTaxonAssigner({})
a(seq_path=self.tmp_seq_filepath,
result_path=None,
log_path=self.tmp_log_filepath)
# open the actual log file and the expected file, and pass into lists
obs = [l.strip() for l in list(open(self.tmp_log_filepath, 'r'))]
exp = rdp_test1_log_file_contents.split('\n')
# sort the lists as the entries are written from a dict,
# so order may vary
obs.sort()
exp.sort()
self.assertEqual(obs, exp)
rdp_test1_fasta = \
""">X67228 some description
aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
>EF503697
TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC
"""
rdp_test1_log_file_contents = \
"""RdpTaxonAssigner parameters:
Application:RDP classfier
Citation:Wang, Q, G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol. 73(16):5261-7.
Taxonomy:RDP
Confidence:0.8
id_to_taxonomy_fp:None
reference_sequences_fp:None"""
rdp_test1_expected_dict = {\
'X67228 some description': ('Root;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium',0.95),\
'EF503697': ('Root;Archaea;Crenarchaeota;Thermoprotei',0.88)
}
rdp_trained_test1_expected_dict = {
'X67228 some description': ('Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium', 1.0),
'EF503697': ('Bacteria;Proteobacteria;Gammaproteobacteria', 0.83999999999999997),
}
rdp_test1_expected_lines = [\
"\t".join(["X67228 some description",\
"Root;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium",\
"0.9"]),
"\t".join(['EF503697','Root;Archaea;Crenarchaeota;Thermoprotei','0.8'])]
rdp_id_to_taxonomy = \
"""X67228 Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium
X73443 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
AB004750 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
xxxxxx Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas
AB004748 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
AB000278 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium
AB000390 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio
"""
rdp_reference_seqs = \
""">X67228
aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
>X73443
nnnnnnngagatttgatcctggctcaggatgaacgctggccggccgtgcttacacatgcagtcgaacgaagcgcttaaactggatttcttcggattgaagtttttgctgactgagtggcggacgggtgagtaacgcgtgggtaacctgcctcatacagggggataacagttagaaatgactgctaataccnnataagcgcacagtgctgcatggcacagtgtaaaaactccggtggtatgagatggacccgcgtctgattagctagttggtggggt
>AB004750
acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgca
>xxxxxx
ttgaacgctggcggcaggcctaacacatgcaagtcgagcggcagcannnncttcgggaggctggcgagcggcggacgggtgagtaacgcatgggaacttacccagtagtgggggatagcccggggaaacccggattaataccgcatacgccctgagggggaaagcgggctccggtcgcgctattggatgggcccatgtcggattagttagttggtggggtaatggcctaccaaggcgacgatccgtagctggtctgagaggatgatcagccacaccgggactgagacacggcccggactcctacgggaggcagcagtggggaatattggacaatgggggcaaccctgatccagccatgccg
>AB004748
acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggccttcgggttg
>AB000278
caggcctaacacatgcaagtcgaacggtaanagattgatagcttgctatcaatgctgacgancggcggacgggtgagtaatgcctgggaatataccctgatgtgggggataactattggaaacgatagctaataccgcataatctcttcggagcaaagagggggaccttcgggcctctcgcgtcaggattagcccaggtgggattagctagttggtggggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggggaaaccctgatgcagccatgccgcgtgta
>AB000390
tggctcagattgaacgctggcggcaggcctaacacatgcaagtcgagcggaaacgantnntntgaaccttcggggnacgatnacggcgtcgagcggcggacgggtgagtaatgcctgggaaattgccctgatgtgggggataactattggaaacgatagctaataccgcataatgtctacggaccaaagagggggaccttcgggcctctcgcttcaggatatgcccaggtgggattagctagttggtgaggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgag
"""
rdp_expected_taxonomy = \
"""1*Bacteria*0*0*domain
2*Firmicutes*1*1*phylum
3*Clostridia*2*2*class
4*Clostridiales*3*3*order
5*Clostridiaceae*4*4*family
6*Clostridium*5*5*genus
7*Proteobacteria*1*1*phylum
8*Alphaproteobacteria*7*2*class
9*Rhizobiales*8*3*order
10*Rhizobiaceae*9*4*family
11*Rhizobium*10*5*genus
12*Gammaproteobacteria*7*2*class
13*Enterobacteriales*12*3*order
14*Enterobacteriaceae*13*4*family
15*Enterobacter*14*5*genus
16*Pseudomonadales*12*3*order
17*Pseudomonadaceae*16*4*family
18*Pseudomonas*17*5*genus
19*Vibrionales*12*3*order
20*Vibrionaceae*19*4*family
21*Photobacterium*20*5*genus
22*Vibrio*20*5*genus
"""
# newline at the end makes a difference
rdp_expected_training_seqs = \
""">AB000278 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium
caggcctaacacatgcaagtcgaacggtaanagattgatagcttgctatcaatgctgacgancggcggacgggtgagtaatgcctgggaatataccctgatgtgggggataactattggaaacgatagctaataccgcataatctcttcggagcaaagagggggaccttcgggcctctcgcgtcaggattagcccaggtgggattagctagttggtggggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggggaaaccctgatgcagccatgccgcgtgta
>AB000390 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio
tggctcagattgaacgctggcggcaggcctaacacatgcaagtcgagcggaaacgantnntntgaaccttcggggnacgatnacggcgtcgagcggcggacgggtgagtaatgcctgggaaattgccctgatgtgggggataactattggaaacgatagctaataccgcataatgtctacggaccaaagagggggaccttcgggcctctcgcttcaggatatgcccaggtgggattagctagttggtgaggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgag
>AB004748 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggccttcgggttg
>AB004750 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgca
>X67228 Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium
aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
>X73443 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
nnnnnnngagatttgatcctggctcaggatgaacgctggccggccgtgcttacacatgcagtcgaacgaagcgcttaaactggatttcttcggattgaagtttttgctgactgagtggcggacgggtgagtaacgcgtgggtaacctgcctcatacagggggataacagttagaaatgactgctaataccnnataagcgcacagtgctgcatggcacagtgtaaaaactccggtggtatgagatggacccgcgtctgattagctagttggtggggt
>xxxxxx Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas
ttgaacgctggcggcaggcctaacacatgcaagtcgagcggcagcannnncttcgggaggctggcgagcggcggacgggtgagtaacgcatgggaacttacccagtagtgggggatagcccggggaaacccggattaataccgcatacgccctgagggggaaagcgggctccggtcgcgctattggatgggcccatgtcggattagttagttggtggggtaatggcctaccaaggcgacgatccgtagctggtctgagaggatgatcagccacaccgggactgagacacggcccggactcctacgggaggcagcagtggggaatattggacaatgggggcaaccctgatccagccatgccg"""
id_to_taxonomy_string = \
"""AY800210\tArchaea;Euryarchaeota;Halobacteriales;uncultured
EU883771\tArchaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.
EF503699\tArchaea;Crenarchaeota;uncultured;uncultured
DQ260310\tArchaea;Euryarchaeota;Methanobacteriales;Methanobacterium
EF503697\tArchaea;Crenarchaeota;uncultured;uncultured"""
test_seq_coll = LoadSeqs(data=[\
('s1','TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC'),\
('s2','TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA'),\
('s3','AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG'),\
('s4','GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT'),\
('s5','TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC'),\
('s6','ATAGTAGGTGATTGCGAAGACCGCGGAACCGGGACCTAGCACCCAGCCTGTACCGAGGGATGGGGAGCTGTGGCGGTCCACCGACGACCCTTTGTGACAGCCGATTCCTACAATCCCAGCAACTGCAATGATCCACTCTAGTCGGCATAACCGGGAATCGTTAACCTGGTAGGGTTCTCTACGTCTGAGTCTACAGCCCAGAGCAGTCAGGCTACTATACGGTTTGCTGCATTGCATAGGCATCGGTCGCGGGCACTCCTCGCGGTTTCAGCTAGGGTTTAAATGGAGGGTCGCTGCATGAGTATGCAAATAGTGCCACTGCTCTGATACAGAGAAGTGTTGATATGACACCTAAGACCTGGTCACAGTTTTAACCTGCCTACGCACACCAGTGTGCTATTGATTAACGATATCGGTAGACACGACCTTGGTAACCTGACTAACCTCATGGAAAGTGACTAGATAAATGGACCGGAGCCAACTTTCACCCGGAAAACGGACCGACGAATCGTCGTAGACTACCGATCTGACAAAATAAGCACGAGGGAGCATGTTTTGCGCAGGCTAGCCTATTCCCACCTCAAGCCTCGAGAACCAAGACGCCTGATCCGGTGCTGCACGAAGGGTCGCCTCTAGGTAAGGAGAGCTGGCATCTCCAGATCCGATATTTTACCCAACCTTTGCGCGCTCAGATTGTTATAGTGAAACGATTTAAGCCTGAACGGAGTTCCGCTCCATATGTGGGTTATATATGTGAGATGTATTAACTTCCGCAGTTGTCTCTTTCGGTGCAGTACGCTTGGTATGTGTCTCAAATAATCGGTATTATAGTGATCTGAGAGGTTTTAAG')],aligned=False)
test_refseq_coll = LoadSeqs(data=[\
('AY800210','TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC'),\
('EU883771','TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA'),\
('EF503699','AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG'),\
('DQ260310','GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT'),\
('EF503697','TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC')],aligned=False)
#run unit tests if run from command-line
if __name__ == '__main__':
main()