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#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
from shutil import rmtree
from glob import glob
from os import getenv
from os.path import basename, exists, join
from tempfile import NamedTemporaryFile
from cogent import LoadSeqs
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import remove_files, create_dir
from qiime.util import (get_qiime_temp_dir,
get_tmp_filename)
from qiime.test import initiate_timeout, disable_timeout
from qiime.parse import fields_to_dict
from qiime.parallel.blast import ParallelBlaster
class ParallelBlasterTests(TestCase):
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_parallel_blaster_tests_',
suffix='',
result_constructor=str)
self.dirs_to_remove.append(self.test_out)
create_dir(self.test_out)
self.tmp_seq_filepath = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_parallel_blaster_tests_input',
suffix='.fasta')
seq_file = open(self.tmp_seq_filepath, 'w')
seq_file.write(blast_test_seqs)
seq_file.close()
self.files_to_remove.append(self.tmp_seq_filepath)
self.reference_seqs_file = NamedTemporaryFile(
prefix='qiime_parallel_blaster_tests_ref_seqs',
suffix='.fasta',dir=tmp_dir)
self.reference_seqs_file.write(blast_ref_seqs)
self.reference_seqs_file.seek(0)
initiate_timeout(60)
def tearDown(self):
""" """
disable_timeout()
remove_files(self.files_to_remove)
# remove directories last, so we don't get errors
# trying to remove files which may be in the directories
for d in self.dirs_to_remove:
if exists(d):
rmtree(d)
def test_parallel_blaster(self):
"""Test ParallelBlaster functions as expected."""
params = {'refseqs_path':self.reference_seqs_file.name,
'disable_low_complexity_filter':False,
'e_value':0.001,
'num_hits':1,
'word_size':30,
'suppress_format_blastdb':False,
'blastmat_dir':None
}
app = ParallelBlaster()
r = app(self.tmp_seq_filepath,
self.test_out,
params,
job_prefix='BLASTTEST',
poll_directly=True,
suppress_submit_jobs=False)
# Basic sanity checks: we should get two blast hits (lines). We ignore
# all of the comments in the file. Each line should have 12 fields
# separated by tabs.
results = [line for line in open(glob(
join(self.test_out, '*_blast_out.txt'))[0], 'U') if not
line.startswith('#')]
self.assertEqual(len(results), 2)
self.assertEqual(len(results[0].split('\t')), 12)
self.assertEqual(len(results[1].split('\t')), 12)
blast_test_seqs = \
""">11472286
GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG
>11472384
AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAAACGCCGTGGTTAATACCCGTGGCGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTCGGGTCTTCATTGACTTGGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTATGGAATCCTGCTGAGAGGTGGGAGTGCCCGAAAGGGAGCCATAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCCTAGTTGCTACGCAAGAGCACTCTAGGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTCGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCACTCTGCAACTCGAGTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTCGAGCGAACGTGTCGAACGTTGAGCGCTCACGCTTATCGGCTGTGAAATTAGGACAGTAAGTCAGACAGACTGAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGATGGTTCGAATCCATCCAGACCCACCATTGTCT
>11468680
TAAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGTGCTTGCACCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACATGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGATCTACGGATGAAAGCGGGGGACCTTCGGGCCTCGCGCTATAGGGTTGGCCGATGGCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCCTTGGCTCTAATACAGTCGGGGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGCTAAGACCGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTGGTGACTGGCAGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGGTCGGAATCCCGCTGAGAGGTGGGAGTGCTCGAAAGAGAACCGGCGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTTAGTTGCTACGCAAGAGCACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCCCAGAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCCAGAGCTATCTCGCAAAGTTGAGCGCTCACGCTTATCGGCTGTAAATTTAAAGACAGACTCAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGTTGGTTCGAATCCAACCAGACCCACCATTGTCTG
>11458037
GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGTTTCGAAGATCGGACTTCGAATTTCGAATTTCGATCATCGAGATAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTACCCATAAAGCCGGGACAACCCTTGGAAACGAGGGCTAATACCGGATAAGCTTGAGAAGTGGCATCACTTTTTAAGGAAAGGTGGCCGATGAGAATGCTGCCGATTATGGATGGACCCGCGTCTGATTAGCTGGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGTATGATGAAGGTTTTCGGATTGTAAAGTACTGTCTATGGGGAAGAATGGTGTGCTTGAGAATATTAAGTACAAATGACGGTACCCAAGGAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGATAGTTAAGTCCGGTGTGAAAGATCAGGGCTCAACCCTGAGAGTGCATCGGAAACTGGGTATCTTGAGGACAGGAGAGGAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTGCTAGGTGTAGAGGGTATCGACCCCTTCTGTGCCGCAGTTAACACAATAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCAGGGCTTGACATCCTCTGAACTTGCTGGAAACAGGAAGGTGCCCTTCGGGGAGCAGAGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAATCCCGCAACGAGCGCAACCCCTGTATTTAGTTGCTAACGCGTAGAGGCGAGCACTCTGGATAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTTCTGGGCTACACACGTGCTACAATGGCCGGTACAGACGGAAGCGAAGCCGCGAGGCGGAGCAAATCCGAGAAAGCCGGTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCTGCAACACCCGAAGCCGGTGAGGTAACCGACTCGAGATTCGAGGCTCGAAGTTCGAGGATCGAAGTGTAAGCGAAATTAATAAGTCTTAGTAAAGCTAAAAAGCATTAAGACCGATAAGATGATCTTGCAATCGAACATCGAACATCGAATTTCGAACCTCGAGTTGGAGCTAGCCGTCGAAGGTGGGGCCGATAATTGGGGTG
>11469739
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCTAACTTCTGATTCCTTCGGGATGATGAGGTTAGCAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTGGGGGATAACCCTCCGAAAGGAGGGCTAATACCGCATAATATCTTTATCCCAAAAGAGGTAAAGATTAAAGATGGCCTCTATACTATGCTATCGCTTCAGGATGAGTCCGCGTCCTATTAGTTAGTTGGTGGGGTAATGGCCTACCAAGACGACAATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGACAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCCTTGGGTTGTAAAATCCTGTTCTGGGGGAAGAAAGCTTAAAGGTCCAATAAACCCTTAAGCCTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTCTTAAAAGTCAGTTGTGAAATTATCAGGCTCAACCTGATAAGGTCATCTGAAACTCTAAGACTTGAGGTTAGAAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTATCTCTGACGCTGAGGAGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGTAGCTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGACTTGACATTATCTTGCCCGTCTAAGAAATTAGATCTTCTTCCTTTGGAAGACAGGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTGTGCTTAGTTGCTAACTTGTTTTACAAGTGCACTCTAGGCAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTTAAGCCAATCCCAAAAAGCAGGCCCCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTAGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTTGGCGATACCTGAAGTTACTAGGCTAACCTGGCACTCAACTAAGTTCACTAACTTATTTGCTTAAAATAAGGCTTAATGTGCTTAGTTGAGTGCCGGGAGGCAGGTACCGAAGGTATGGCTGGCGATTGGGGTGAAGTCGTAACAAGGTGGAAA
>11469752
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGCAGCGAGTTCCTCACCGAGGTTCGGAACAGTTGACAGTAAACAGTTGACAGTAAACAGTAACTTCAGAAATGAAGCGGACTGTGAACTGTTTACTGTAACCTGTTAGCTATTATTTCGAGCTTTAGTGAGGAATGTCGGCGAGCGGCGGACGGCTGAGTAACGCGTAGGAACGTACCCCAAACTGAGGGATAAGCACCAGAAATGGTGTCTAATACCGCATATGGCCCAGCACCTTTTTTAATCAACCACGACCCTAAAATCGTGAATAATTGGTAGGAAAAGGTGTTGGGTTAAAGCTTCGGCGGTTTGGGAACGGCCTGCGTATGATTAGCTTGTTGGTGAGGTAAAAGCTCACCAAGGCGACGATCATTAGCTGGTCTGAGAGGATGATCAGCCAGACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGTGTGCAGGATGAAAGCCTTCGGGTCGTAAACTGCTTTTATATGTGAAGACTTCGACGGTAGCATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTCATACGGAGGATCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGTTGGTAGTGAAATTGTGTGGCTCAACCATACACCCATTACTAAAACTGCTAAGCTAGAGTATATGAGAGGTAGCTGGAATTCCTAGTGTAGGAGTGAAATCCGTANATATTAGGAGGAACACCGATGGCGTAGGCAGGCTACTGGCATATTACTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCTGTAAACGATGGATGCTAGCTGTTATGAGTATCGACCCTTGTAGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACGAGCGCAAGCTTAAAACATAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGATGATAAGCGAAGAACCTTACCAAGGCTTGACATCCCTGGAATTTCTCCGAAAGGAGAGAGTGCCTTCGGGAATCAGGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATTAACGAGCGCAACCCTTGTAAATAGTTGGATTTTTCTATTTAGACTGCCTCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCAGTATTTCTCTTACGCCTTGGGCTACAAACACGCTACAATGGCCGGTACAAAGGGCAGCCAACCCGCGAGGGGGAGCAAATCCCATCAAAGCCGGTCTCAGTTCGGATAGCAGGCTGAAATTCGCCTGCTTGAAGTCGGAATCGCTAGTAACGGTGAGTCAGCTATATTACCGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCAAGGCATGAAAGTCATCAATACCTGACGTCTGGATTTATTCTGGCCTAAGGTAGGGGCGATGATTGGGCCTAAGTCGTAACAAGGTAA
>11460523
AGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCGAAATCGGGCACTCAATTTTGCTTTTCAAACATTAACTGATGAAACGACCAGAGAGATTGTTCCAGTTTAAAGAGTGAAAAGCAGGCTTGAGTGCCTGAGAGTAGAGTGGCGCACGGGTGAGTAACGCGTAAATAATCTACCCCTGCATCTGGGATAACCCACCGAAAGGTGAGCTAATACCGGATACGTTCTTTTAACCGCGAGGTTTTAAGAAGAAAGGTGGCCTCTGATATAAGCTACTGTGCGGGGAGGAGTTTGCGTACCATTAGCTAGTTGGTAGGGTAATGGCCTACCAAGGCATCGATGGTTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGGAACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTCGTAAAATCCTGTCAGATGGAAAGAAGTGTTATATGGATAATACCTGTATAGCTTGACGGTACCATCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTCTGTTATGTCAGATGTGAAAGTCCACGGCTCAACCGTGGAAGTGCATTTGAAACTGACAGACTTGAGTACTGGAGGGGGTGGTGGAATTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAATACCGGTGGCGAAGGCGACCACCTGGCCAGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGGTGTTGGGATGGTTAATCGTCTCATTGCCGGAGCTAACGCATTAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCTGGTCTTGACATCCCGAGAATCTCAAGGAAACTTGAGAGTGCCTCTTGAGGAACTCGGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTTTAGTTGCCATCATTAAGTTGGGCACTCTAAAGAGACTGCCGGTGTCAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTACACACGTACTACAATGGCATAGACAAAGGGCAGCGACATCGCGAGGTGAAGCGAATCCCATAAACCATGTCTCAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGGGAGTTGGTTGTACCAGAAGCAGTTGAGCGAACTATTCGTAGACGCAGGCTGCCAAGGTATGATTGGTAACTGGGGTGAAGTCGTAACAAGGTAACC
>11460543
TGGTTTGATCCTGGCTCAGGACAAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCCAGCTTTTGATTCCTTCGGGATGAGAAAGCAGGTAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTAGGGGATAACCCTCTGAAAAGAGGGCTAATACCGCATAATATCTTTACCCCATAAGAAGTAAAGATTAAAGATGGCCTCTGTATATGCTATCGCTTCAGGATGAGCCCGCGTCCTATTAGTTAGTTGGTAAGGTAATGGCTTACCAAGACCACGATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTTGTAAAATCCTGTTTTGGGGGACGAAACCTTAAGGGTCCAATAAACCCTTAAATTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGTTCGTAGGCGGTCTTAAAAGTCAGGTGTGAAATTATCAGGCTTAACCTGATACGGTCATCTGAAACTTTAAGACTTGAGGTTAGGAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGCCTAACTCTGACGCTGAGGAACGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGWCACTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGGCTTGACATTGTCTTGCCCGTTTAAGAAATTAAATTTTCTTCCCTTTTAGGGAAGACAAGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTATTCTTAGTTGCTAGTTTGTTTACAAACGCACTCTAAAGAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTCAAGCTAATCCCTTAAAACAGGTCTCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAAAGTTGGCGATACCTGAAGTTACTGTGCTAACCCGGCACTCAACTAAGTACATTAAGTCTTATTTTAAGCTATTGTATTTAGTTGAGTGCCGGGAGGCAGGTACCTAAGGTATGGCTAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCG
>11480235
TGGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGCGCCTTATACATGCAAGTCGAACGAGCCTTGTGCTTCGCACAAGGAAATTCCAAGCACCAAGCACCAAATCTCAAACAAATCCCAATGACCAAAATTCCAAAAACCTAAACATTTTAAATGTTTAGAATTTGGAAAATTGGAATTTGGAATTTATTTGTTATTTGGAATTTATGATTTGGGATTTTCTCGCGCGGAGANCNTNAGTGGCGAACGGGTGAGTAATACGTTGGTATCTACCCCAAAGTAGAGAATAAGCCCGAGAAATCGGGGTTAATACTCTATGTGTTCGAAAGAACAAAGACTTCGGTTGCTTTGGGAAGAACCTGCGGCCTATCAGCTTGTTGGTAAGGTAACGGCTTACCAAGGCTTTGACGGGTAGCTGGTCTGGGAAGACGACCAGCCACAATGGGACTTAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGCCCGAAAGGTGACCGAGCGACGCCGCGTAGAGGAAGAAGATCTTTGGATTGTAAACTCTTTTTCTCCTAGACAAAGTTCTGATTGTATAGGAGGAATAAGGGGTTTCTAAACTCGTGCCAGCAGAAGCGGTAATACGAGTGCCCCAAGCGTTATCCGGAATCATTGGGCGTAGAGCGTTGTATAGGTGGTTTAAAAAGTCCAAAATTAAATCTTTAGGCTCAACCTAAAATCTGTTTTGGAAACTTTTAGACTTGAATAAAATCGACGSGAGTGGAACTTCCAGAGTAGGGGTTACATCCGTTGATACTGGAAGGAACGCCGAAGGCGAAAGCAACTCGCGAGATTTTATTGACGCCGCGTACACGAAAGCGTGGGGAGCGAAAAGTATTAGATACACTTGTAGTCCACGCCGTAAACTATGGATACTAGCAATTTGAAGCTTCGACCCTTCAAGTTGCGGACTAACGCGTTAAGTATCTCGCCTGGGAAGTACGGCCGCAAGGCTAAAACTCAAAGGAATAGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGATAAGCGTGGAACCTTACCAGGGCTTAGACGTACAGAGAATTCCTTGGAAACAAGGAAGTGCTTCGGGAACTCTGTACTCAGGTACTGCATGGCTGTCGTCAGTATGTACTGTGAAGCACTCCCTTAATTGGGGCAACATACGCAACCCCTATCCTAAGTTAGAAATGTCTTAGGAAACCGCTTCGATTCATCGGAGAGGAAGATGGGGACGACGTCAAGTCAGCATGGTCCTTGATGTCCTGGGCGACACACGTGCTACAATGGCTAGTATAACGGGATGCGTAGGTGCGAACCGAAGCTAATCCTTAAAAAACTAGTCTAAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCCGGAATCGCTAGTAACCGCAAATCAGCCACGTTGCGGTGAATACGTTCTCGGGCCTTGTACTCACTGCCCGTCACGTCAAAAAAGTCGGTAATACCCGAAGCACCCTTTTAAAGGGTTCTAAGGTAGGACCGATGATTGGGACGAAGTCGTAACAAGGTAGCCG
>11480408
AATTTAGCGGCCGCGAATTCGCCCTTGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGGATATCCGAGCGGAAGGTTTCGGCCGGAAGGTTGGGTATTCGAGTGGCGGACGGGTGAGTAACGCGTGAGCAATCTGTCCCGGACAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAAGACCACAGCATCGCATGGTGCAGGGGTAAAAGGAGCGATCCGGTCTGGGGTGAGCTCGCGTCCGATTAGATAGTTGGTGAGGTAACGGCCCACCAAGTCAACGATCGGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGAACTGAGAGACGGTCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTTATGCGAGACGAAGGAAGTGACGGTATCGCATAAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGTGTAGGCGGCCGTTTAAGTATGGAGTGAAAGTCCATTTTTCAAGGATGGAATTGCTTTGTAGACTGGATGGCTTGAGTGCGGAAGAGGTAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGAGGAACACCAGTGGCGAAGGCGACTTACTGGGCCGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCGGTAAACGATGAATGCTAGGTGTTGCGGGTATCGACCCCTGCAGTGCCGGAGTAAACACAATAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAGGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTTGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCAGTTAAGCTCATAGAGATATGAGGTCCCTTCGGGGGAACTGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATGGTCAGTTACTAACGCGTGAAGGCGAGGACTCTGACGAGACTGCCGGGGACAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGCTACAATGGTGACTACAAAGAGGAGCGAGACTGTAAAGTGGAGCGGATCTCAAAAAAGTCATCCCAGTTCGGATTGTGGGCTGCAACCCGCCCACATGAAGTTGGAGTTGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGGAGCACCCGAAGTCAGTGAGGTAACCGGAAGGAGCCAGCTGCCGAAGGTGAGACCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTAAGGGCGAATTCGTTTAAACCTGCAGGACTAG
"""
blast_ref_seqs = \
"""
>AY800210
TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC
>EU883771
TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA
>EF503699
AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG
>DQ260310
GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT
>EF503697
TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC
"""
if __name__ == "__main__":
main()
|
