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test_map_reads_to_reference.py
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test_map_reads_to_reference.py
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#!/usr/bin/env python
# File created on 13 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from os import close
from shutil import rmtree
from os.path import exists, join
from tempfile import mkstemp , mkdtemp
from skbio.util import remove_files
from unittest import TestCase, main
from numpy.testing import assert_almost_equal
from biom import load_table
from qiime.util import get_qiime_temp_dir
from qiime.map_reads_to_reference import (
usearch_database_mapper, blat_database_mapper, bwa_short_database_mapper,
bwa_sw_database_mapper, blat_nt_database_mapper)
from qiime.parse import parse_otu_map
from qiime.test import initiate_timeout, disable_timeout
class DatabaseAssignmentTests(TestCase):
"""
"""
def setUp(self):
"""
"""
tmp_dir = get_qiime_temp_dir()
self.test_out = mkdtemp(dir=tmp_dir,
prefix='qiime_parallel_tests_',
suffix='')
self.dirs_to_remove = [self.test_out]
self.output_fp = join(self.test_out, 'fmap.txt')
self.failure_fp = join(self.test_out, 'fail.txt')
self.usearch_fp = join(self.test_out, 'out.uc')
self.bl6_fp = join(self.test_out, 'out.bl6')
self.log_fp = join(self.test_out, 'fmap.log')
self.files_to_remove = [self.output_fp, self.failure_fp,
self.usearch_fp, self.log_fp, self.bl6_fp]
fd, self.refseqs1_fp = mkstemp(dir=self.test_out,
prefix='qiime_refseqs',
suffix='.fasta')
close(fd)
refseqs1_f = open(self.refseqs1_fp, 'w')
refseqs1_f.write(refseqs1)
refseqs1_f.close()
self.files_to_remove.append(self.refseqs1_fp)
fd, self.refseqs2_fp = mkstemp(dir=self.test_out,
prefix='qiime_refseqs',
suffix='.fasta')
close(fd)
refseqs2_f = open(self.refseqs2_fp, 'w')
refseqs2_f.write(refseqs2)
refseqs2_f.close()
self.files_to_remove.append(self.refseqs2_fp)
fd, self.inseqs1_fp = mkstemp(dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
close(fd)
inseqs1_f = open(self.inseqs1_fp, 'w')
inseqs1_f.write(inseqs1)
inseqs1_f.close()
self.files_to_remove.append(self.inseqs1_fp)
fd, self.inseqs2_fp = mkstemp(dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
close(fd)
inseqs2_f = open(self.inseqs2_fp, 'w')
inseqs2_f.write(inseqs2)
inseqs2_f.close()
self.files_to_remove.append(self.inseqs2_fp)
initiate_timeout(60)
def tearDown(self):
""" """
disable_timeout()
remove_files(self.files_to_remove, error_on_missing=False)
# 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)
class UsearchDatabaseAssignmentTests(DatabaseAssignmentTests):
def test_usearch_database_mapper(self):
"""usearch_database_mapper functions as expected """
usearch_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=0.75,
queryalnfract=0.35,
targetalnfract=0.0,
maxaccepts=1,
maxrejects=8,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(
table.ids(axis='observation'),
['eco:b0122-pr',
'eco:b0015-pr'])
self.assertEqual(table.sum(), 5)
class BlatDatabaseAssignmentTests(DatabaseAssignmentTests):
def test_blat_database_mapper(self):
"""blat_database_mapper functions as expected """
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=0.75,
genetic_code=11,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(
table.ids(axis='observation'),
['eco:b0122-pr',
'eco:b0015-pr'])
self.assertEqual(table.sum(), 5)
def test_blat_database_mapper_alt_params(self):
"""blat_database_mapper functions as expected w alt e-value"""
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-2,
min_id=0.75,
genetic_code=2,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(table.ids(axis='observation'),
['eco:b0122-pr', 'eco:b0015-pr', 'eco:b0001-pr'])
self.assertEqual(table.sum(), 6)
class BlatNtAssignmentTests(DatabaseAssignmentTests):
def test_blat_nt_database_mapper(self):
"""blat_nt_database_mapper functions as expected """
blat_nt_database_mapper(query_fp=self.inseqs2_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=0.75,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(
table.ids(axis='observation'),
['r1',
'r2',
'r3',
'r4',
'r5'])
self.assertEqual(table.sum(), 6)
def test_blat_nt_database_mapper_alt_min_id(self):
"""blat_nt_database_mapper functions as expected """
blat_nt_database_mapper(query_fp=self.inseqs2_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=1.0,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(table.ids(axis='observation'),
['r2', 'r3', 'r4', 'r5'])
self.assertEqual(table.sum(), 5)
class BwaShortAssignmentTests(DatabaseAssignmentTests):
def test_bwa_short_database_mapper(self):
"""bwa_short_database_mapper functions as expected """
bwa_short_database_mapper(query_fp=self.inseqs2_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
max_diff=None,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(
table.ids(axis='observation'),
['r1',
'r2',
'r3',
'r4',
'r5'])
self.assertEqual(table.sum(), 6)
def test_bwa_short_database_mapper_alt_params(self):
"""bwa_short_database_mapper functions as expected """
bwa_short_database_mapper(query_fp=self.inseqs2_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
max_diff=1,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(table.ids(axis='observation'),
['r2', 'r3', 'r4', 'r5'])
self.assertEqual(table.sum(), 5)
# float can also be passed for max_diff
bwa_short_database_mapper(query_fp=self.inseqs2_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
max_diff=0.01,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
class BwaSwAssignmentTests(DatabaseAssignmentTests):
def test_bwa_sw_database_mapper(self):
"""bwa_sw_database_mapper functions as expected """
bwa_sw_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs2_fp,
output_dir=self.test_out,
HALT_EXEC=False)
observation_map_fp = join(self.test_out, 'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out, 'observation_table.biom')
table = load_table(observation_table_fp)
self.assertItemsEqual(table.ids(), ['s2', 's1'])
self.assertItemsEqual(
table.ids(axis='observation'),
['r1',
'r2',
'r3',
'r4',
'r5'])
self.assertEqual(table.sum(), 6)
refseqs1 = """>eco:b0001-pr
MKRISTTITTTITITTGNGAG
>eco:b0015-pr dnaJ
MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDS
QKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYN
MELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQ
QTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAP
AGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTG
KLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRS
KSFFDGVKKFFDDLTR
>eco:b0122-pr
MKTFFRTVLFGSLMAVCANSYALSESEAEDMADLTAVFVFLKNDCGYQNLPNGQIRRALV
FFAQQNQWDLSNYDTFDMKALGEDSYRDLSGIGIPVAKKCKALARDSLSLLAYVK
"""
refseqs2 = """>r1
atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
ggctga
>r2 some comments...
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgagaa
>r3
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>r4
atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc
>r5 some comments...
aatgactaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
inseqs1 = """>s1_1
atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
ggctga
>s2_2 some comments...
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgagaa
>s1_3
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>s1_4
atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc
>s1_5
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
>s1_6 some comments...
aatgactaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
inseqs2 = """>s1_1
atgaaacgcattagcaccaccattaccaccattatcaccattaccacaggtaacggtgcg
ggctga
>s2_2 some comments...
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgagaa
>s1_3
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>s1_4
atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc
>s1_5
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
>s1_6 some comments...
aatgactaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
if __name__ == "__main__":
main()