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test_identify_chimeric_seqs.py
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test_identify_chimeric_seqs.py
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#!/usr/bin/env python
# File created on 06 Oct 2009.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2010, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "0.92"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from os.path import exists, split, splitext
from cogent import LoadSeqs, DNA
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import remove_files
from cogent.app.util import get_tmp_filename
from qiime.pycogent_backports.formatdb import build_blast_db_from_fasta_file
from qiime.identify_chimeric_seqs import BlastFragmentsChimeraChecker
class BlastFragmentsChimeraCheckerTests(TestCase):
""" """
def setUp(self):
""" """
self.id_to_taxonomy_fp = get_tmp_filename(\
prefix='BlastFragmentsChimeraCheckerTests_',suffix='.txt')
self.input_seqs_fp = get_tmp_filename(\
prefix='BlastFragmentsChimeraCheckerTests_',suffix='.fasta')
self.reference_seqs_fp = get_tmp_filename(\
prefix='BlastFragmentsChimeraCheckerTests_',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())
open(self.reference_seqs_fp,'w').write(test_refseq_coll.toFasta())
self.bcc = None
self.expected1 = [\
('c1',\
['Archaea;Euryarchaeota;Halobacteriales;uncultured',\
'Archaea;Crenarchaeota;uncultured;uncultured'])]
def tearDown(self):
remove_files(self._paths_to_clean_up)
if self.bcc != None:
self.bcc.cleanUp()
def test_init_creates_db(self):
"""BlastFragmentsChimeraCheckerTests: blast database created/cleaned
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
self.assertEqual(self.bcc.num_fragments,3)
# blast db created
db_name = split(self.reference_seqs_fp)[1]
db_fp = '/tmp/%s.nsq' % db_name
self.assertTrue(exists(db_fp))
self.bcc.cleanUp()
# db is cleaned up
self.assertFalse(exists(db_fp))
def test_init_creates_db(self):
"""BlastFragmentsChimeraChecker: parameters initialized correctly
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp,\
'num_fragments':2}
self.bcc = BlastFragmentsChimeraChecker(params)
self.assertEqual(self.bcc.Params['num_fragments'],2)
def test_function_w_preexisting_blastdb(self):
blast_db, db_files_to_remove = \
build_blast_db_from_fasta_file(test_refseq_coll.toFasta().split('\n'))
self._paths_to_clean_up += db_files_to_remove
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':None,\
'blast_db':blast_db,\
'num_fragments':2}
self.bcc = BlastFragmentsChimeraChecker(params)
actual = list(self.bcc(self.input_seqs_fp))
self.assertEqual(actual,self.expected1)
def test_fragmentSeq_even_len_frags(self):
"""BlastFragmentsChimeraChecker:_fragment_seq fns when frags are evenly divisible
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
# default: 3 frags
self.assertEqual(self.bcc._fragment_seq('ACCGTTATATTT'),\
['ACCG','TTAT','ATTT'])
self.bcc.Params['num_fragments'] = 2
self.assertEqual(self.bcc._fragment_seq('ACCGTTATATTT'),\
['ACCGTT','ATATTT'])
self.bcc.Params['num_fragments'] = 4
self.assertEqual(self.bcc._fragment_seq('ACCGTTATATTT'),\
['ACC','GTT','ATA','TTT'])
def test_fragment_seq_uneven_len_frags(self):
"""BlastFragmentsChimeraChecker:_fragment_seq fns when frags aren't evenly divisible
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
# default: 3 frags
self.assertEqual(self.bcc._fragment_seq('ACCGTTATATTTC'),\
['ACCGT','TATA','TTTC'])
self.assertEqual(self.bcc._fragment_seq('ACCGTTATATTTCC'),\
['ACCGT','TATAT','TTCC'])
def test_is_chimeric(self):
"""BlastFragmentsChimeraChecker: _is_chimeric functions as expected
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
# Basic cases, fewer than 4 assignments deep
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD','AB;CE','AB;CD']))
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD','AB;CD','AB;CD']))
# Basic cases, exactly 4 assignments deep
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;GH']))
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
# Leading/trialing spaces in taxa don't affect results
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF; GH ','AB ;CD;EF;GH','AB;CD; EF;GH']))
# More complex cases -- only first four levels are considered
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH;IJ','AB;CD;EF;GH']))
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH;LM;XY','AB;CD;EF;GH;IJ','AB;CD;EF;GH;JK']))
# unlikely case (but possible) where 5th level is identical,
# but 4th is not
self.bcc.Params['taxonomy_depth'] = 3
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH;XY','AB;CD;EF;JK;XY','AB;CD;EF;GH;XY']))
self.bcc.Params['taxonomy_depth'] = 4
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD;EF;GH;XY','AB;CD;EF;JK;XY','AB;CD;EF;GH;XY']))
self.bcc.Params['taxonomy_depth'] = 5
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD;EF;GH;XY','AB;CD;EF;JK;XY','AB;CD;EF;GH;XY']))
def test_is_chimeric_no_blast_hit(self):
"""BlastFragmentsChimeraChecker: no blast hit is lack of evidence for chimeric
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
# 'No blast hit' values ignored (lack of evidence to claim sequence
# is chimeric)
self.bcc.Params['taxonomy_depth'] = 3
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF','No blast hit','AB;CD;EF']))
self.assertFalse(self.bcc._is_chimeric(\
['No blast hit','No blast hit','No blast hit']))
self.assertFalse(self.bcc._is_chimeric(\
['No blast hit','AB;CD;EF','AB;CD;EF']))
# Still called a chimera though if other assignments suggest that it is
self.assertTrue(self.bcc._is_chimeric(\
['No blast hit','AB;CD;EF','AB;CD;XY']))
def test_is_chimeric_alt_depth(self):
"""BlastFragmentsChimeraChecker: _is_chimeric functions as expected with alt depth
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
# chimeric at depth 5
self.bcc.Params['taxonomy_depth'] = 5
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
# chimeric at depth 4
self.bcc.Params['taxonomy_depth'] = 4
self.assertTrue(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
# non-chimeric at depth 3
self.bcc.Params['taxonomy_depth'] = 3
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
# non-chimeric at depth 2
self.bcc.Params['taxonomy_depth'] = 2
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
# non-chimeric at depth 1
self.bcc.Params['taxonomy_depth'] = 1
self.assertFalse(self.bcc._is_chimeric(\
['AB;CD;EF;GH','AB;CD;EF;GH','AB;CD;EF;XY']))
def test_get_taxonomy(self):
"""BlastFragmentsChimeraChecker: getTaxonomy functions with full-length sequence
(Just testing the input/output here as the core functionality
is tested in Qiime/tests/test_assign_taxonomy.py.)
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp}
self.bcc = BlastFragmentsChimeraChecker(params)
s1 = test_seq_coll.getSeq('s1')
actual = self.bcc._get_taxonomy(str(s1))
expected = "Archaea;Euryarchaeota;Halobacteriales;uncultured"
self.assertEqual(actual,expected)
def test_call(self):
"""BlastFragmentsChimeraChecker: correct assignments on known results
"""
params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\
'reference_seqs_fp':self.reference_seqs_fp,\
'num_fragments':2}
self.bcc = BlastFragmentsChimeraChecker(params)
actual = list(self.bcc(self.input_seqs_fp))
self.assertEqual(actual,self.expected1)
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_refseq_coll = LoadSeqs(data=[\
('AY800210','TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC'),\
('EU883771','TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA'),\
('EF503699','AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG'),\
('DQ260310','GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT'),\
('EF503697','TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC')],aligned=False)
test_seq_coll = LoadSeqs(data=[\
('s1','TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC'),\
('s2','TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA'),\
('s3','AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG'),\
('s4','GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT'),\
('s5','TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC'),\
('s6','ATAGTAGGTGATTGCGAAGACCGCGGAACCGGGACCTAGCACCCAGCCTGTACCGAGGGATGGGGAGCTGTGGCGGTCCACCGACGACCCTTTGTGACAGCCGATTCCTACAATCCCAGCAACTGCAATGATCCACTCTAGTCGGCATAACCGGGAATCGTTAACCTGGTAGGGTTCTCTACGTCTGAGTCTACAGCCCAGAGCAGTCAGGCTACTATACGGTTTGCTGCATTGCATAGGCATCGGTCGCGGGCACTCCTCGCGGTTTCAGCTAGGGTTTAAATGGAGGGTCGCTGCATGAGTATGCAAATAGTGCCACTGCTCTGATACAGAGAAGTGTTGATATGACACCTAAGACCTGGTCACAGTTTTAACCTGCCTACGCACACCAGTGTGCTATTGATTAACGATATCGGTAGACACGACCTTGGTAACCTGACTAACCTCATGGAAAGTGACTAGATAAATGGACCGGAGCCAACTTTCACCCGGAAAACGGACCGACGAATCGTCGTAGACTACCGATCTGACAAAATAAGCACGAGGGAGCATGTTTTGCGCAGGCTAGCCTATTCCCACCTCAAGCCTCGAGAACCAAGACGCCTGATCCGGTGCTGCACGAAGGGTCGCCTCTAGGTAAGGAGAGCTGGCATCTCCAGATCCGATATTTTACCCAACCTTTGCGCGCTCAGATTGTTATAGTGAAACGATTTAAGCCTGAACGGAGTTCCGCTCCATATGTGGGTTATATATGTGAGATGTATTAACTTCCGCAGTTGTCTCTTTCGGTGCAGTACGCTTGGTATGTGTCTCAAATAATCGGTATTATAGTGATCTGAGAGGTTTTAAG'),\
('c1','TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG')],aligned=False)
if __name__ == "__main__":
main()