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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.app.util import get_tmp_filename
from cogent.app.blat import Blat, assign_reads_to_database, \
assign_dna_reads_to_dna_database, \
assign_dna_reads_to_protein_database
from os.path import join, exists
from os import remove
from re import search
__author__ = "Adam Robbins-Pianka"
__copyright__ = "Copyright 2007-2012, The QIIME Project"
__credits__ = ["Adam Robbins-Pianka", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Adam Robbins-Pianka"
__email__ = "adam.robbinspianka@colorado.edu"
__status__ = "Prototype"
class BlatTests(TestCase):
files_to_remove = []
def setUp(self):
"""Sets up files for testing.
"""
self.test_db_prot_filename = get_tmp_filename().replace('"', '')
self.test_db_prot = open(self.test_db_prot_filename, 'w')
self.test_db_dna_filename = get_tmp_filename().replace('"', '')
self.test_db_dna = open(self.test_db_dna_filename, 'w')
self.test_query_filename = get_tmp_filename().replace('"', '')
self.test_query = open(self.test_query_filename, 'w')
# write the global variables at the bottom of this file to the
# temporary test files. Can't use file-like objects because the
# external application needs actual files.
self.test_db_prot.write('\n'.join(test_db_prot))
self.test_db_dna.write('\n'.join(test_db_dna))
self.test_query.write('\n'.join(test_query))
# close the files
self.test_db_prot.close()
self.test_db_dna.close()
self.test_query.close()
# prepare output file path
self.testout = get_tmp_filename().replace('"', '')
self.files_to_remove += [self.test_db_prot_filename,
self.test_db_dna_filename,
self.test_query_filename, self.testout]
def tearDown(self):
"""Removes temporary files created during the tests
"""
for filename in self.files_to_remove:
if exists(filename): remove(filename)
def test_assign_reads_to_database(self):
"""Tests that assign_reads_to_database works as expected.
Checks the output file against the expected result when known
database and query files are used.
"""
exp = [l for l in assign_reads_exp if not l.startswith('#')]
obs_lines = assign_reads_to_database(self.test_query_filename,
self.test_db_dna_filename,
self.testout).read().splitlines()
obs = [l for l in obs_lines if not l.startswith('#')]
self.assertEqual(obs, exp)
def test_assign_dna_reads_to_dna_database(self):
"""Tests that assign_dna_reads_to_dna_database works as expected.
Checks the output file against the expected result when known
database and query files are used.
"""
exp = [l for l in assign_reads_exp if not l.startswith('#')]
obs_lines = assign_dna_reads_to_dna_database(self.test_query_filename,
self.test_db_dna_filename,
self.testout).read().splitlines()
obs = [l for l in obs_lines if not l.startswith('#')]
self.assertEqual(obs, exp)
def test_assign_dna_reads_to_protein_database(self):
"""Tests that assign_dna_reads_to_protein_database works as expected.
Checks the output file against the expected result when known
database and query files are used.
"""
exp = [l for l in assign_reads_prot_exp if not l.startswith('#')]
obs_lines = assign_dna_reads_to_protein_database(
self.test_query_filename,
self.test_db_prot_filename,
self.testout).read().splitlines()
obs = [l for l in obs_lines if not l.startswith('#')]
self.assertEqual(obs, exp)
def test_get_base_command(self):
"""Tests that _get_base_command generates the proper command given
various inputs.
"""
test_parameters_blank = {}
files = (self.test_query_filename, self.test_db_dna_filename,
self.testout)
exp_blank = 'blat %s %s %s' % (files[1], files[0], files[2])
# initialize a Blat instance with these parameters and get the
# command string
b = Blat(params = {}, HALT_EXEC=True)
# need to set the positional parameters' values
b._input_as_list(files)
cmd = b._get_base_command()
# find the end of the cd command and trim the base command
cmd_index = search('cd ".+"; ', cmd).end()
cmd = cmd[cmd_index:]
self.assertEqual(cmd, exp_blank)
test_parameters_1 = {
'-t': 'dna',
'-q': 'dna',
'-ooc': '11.ooc',
'-tileSize': 1,
'-stepSize': 2,
'-oneOff': 1,
'-minMatch': 2,
'-minScore': 3,
'-minIdentity': 4,
'-maxGap': 5,
'-makeOoc': 'N.ooc',
'-repMatch': 6,
'-mask': 'lower',
'-qMask': 'lower',
'-repeats': 'lower',
'-minRepDivergence': 7,
'-dots': 8,
'-out': 'psl',
'-maxIntron': 9}
exp_1 = 'blat %s %s ' % (files[1], files[0]) + \
'-dots=8 -makeOoc="N.ooc" -mask=lower -maxGap=5 ' + \
'-maxIntron=9 -minIdentity=4 -minMatch=2 ' + \
'-minRepDivergence=7 -minScore=3 -oneOff=1 -ooc="11.ooc" ' + \
'-out=psl -q=dna -qMask=lower -repMatch=6 -repeats=lower ' + \
'-stepSize=2 -t=dna -tileSize=1 %s' % files[2]
# initialize a Blat instance with these parameters and get the
# command string
b = Blat(params = test_parameters_1, HALT_EXEC=True)
# need to set the positional parameters' values
b._input_as_list(files)
cmd = b._get_base_command()
# find the end of the cd command and trim the base command
cmd_index = search('cd ".+"; ', cmd).end()
cmd = cmd[cmd_index:]
self.assertEqual(cmd, exp_1)
test_parameters_2 = {
'-tileSize': 1,
'-stepSize': 2,
'-minMatch': 2,
'-minScore': 3,
'-minIdentity': 4,
'-maxGap': 5,
'-makeOoc': 'N.ooc',
'-out': 'psl',
'-maxIntron': 9}
exp_2 = 'blat %s %s ' % (files[1], files[0]) + \
'-makeOoc="N.ooc" -maxGap=5 -maxIntron=9 -minIdentity=4 ' + \
'-minMatch=2 -minScore=3 -out=psl -stepSize=2 ' + \
'-tileSize=1 %s' % files[2]
# initialize a Blat instance with these parameters and get the
# command string
b = Blat(params = test_parameters_2, HALT_EXEC=True)
# need to set the positional parameters' values
b._input_as_list(files)
cmd = b._get_base_command()
# find the end of the cd command and trim the base command
cmd_index = search('cd ".+"; ', cmd).end()
cmd = cmd[cmd_index:]
self.assertEqual(cmd, exp_2)
assign_reads_exp = """# BLAT 34 [2006/03/10]
# Query: NZ_GG770509_647533119
# Database: test_db.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG770509_647533119 NZ_GG770509_647533119 100.00 1371 0 0 1 1371 1 1371 0.0e+00 2187.0
NZ_GG770509_647533119 NZ_ACIZ01000148_643886127 85.49 634 92 0 336 969 337 970 4.5e-234 807.0
NZ_GG770509_647533119 NZ_ACIZ01000148_643886127 86.08 237 33 0 1135 1371 1137 1373 1.2e-77 287.0
NZ_GG770509_647533119 NZ_ACIZ01000148_643886127 83.12 154 26 0 976 1129 977 1130 2.2e-48 190.0
NZ_GG770509_647533119 NZ_GG739926_647533195 78.42 329 71 0 656 984 657 985 4.8e-97 351.0
NZ_GG770509_647533119 NZ_GG739926_647533195 89.09 110 11 1 1138 1246 1141 1250 1.1e-30 131.0
NZ_GG770509_647533119 NZ_GG739926_647533195 86.96 69 9 0 1021 1089 1023 1091 3.2e-20 96.0
NZ_GG770509_647533119 NZ_GG739926_647533195 75.26 97 22 2 356 450 356 452 2.3e-13 73.0
NZ_GG770509_647533119 NZ_GG739926_647533195 90.57 53 5 0 1319 1371 1315 1367 2.5e-10 63.0
NZ_GG770509_647533119 NZ_GG739926_647533195 81.82 22 4 0 989 1010 992 1013 1.5e+02 24.0
# BLAT 34 [2006/03/10]
# Query: NZ_GG739926_647533195
# Database: test_db.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG739926_647533195 NZ_GG739926_647533195 100.00 1367 0 0 1 1367 1 1367 0.0e+00 2235.0
NZ_GG739926_647533195 NZ_ACIZ01000148_643886127 76.22 572 136 0 414 985 414 985 1.7e-158 556.0
NZ_GG739926_647533195 NZ_ACIZ01000148_643886127 76.80 181 42 0 1023 1203 1022 1202 6.4e-53 205.0
NZ_GG739926_647533195 NZ_ACIZ01000148_643886127 96.00 50 2 0 1209 1258 1207 1256 6.4e-14 75.0
NZ_GG739926_647533195 NZ_ACIZ01000148_643886127 88.68 53 6 0 1315 1367 1321 1373 1.6e-09 61.0
NZ_GG739926_647533195 NZ_ACIZ01000148_643886127 77.27 22 5 0 992 1013 990 1011 8.5e+02 22.0
NZ_GG739926_647533195 NZ_GG770509_647533119 79.29 280 58 0 657 936 656 935 9.9e-82 301.0
NZ_GG739926_647533195 NZ_GG770509_647533119 89.09 110 11 1 1141 1250 1138 1246 1.1e-30 131.0
NZ_GG739926_647533195 NZ_GG770509_647533119 86.96 69 9 0 1023 1091 1021 1089 3.2e-20 96.0
NZ_GG739926_647533195 NZ_GG770509_647533119 75.26 97 22 2 356 452 356 450 2.3e-13 73.0
NZ_GG739926_647533195 NZ_GG770509_647533119 90.57 53 5 0 1315 1367 1319 1371 2.5e-10 63.0
NZ_GG739926_647533195 NZ_GG770509_647533119 80.00 30 6 0 956 985 955 984 1.2e-03 41.0
NZ_GG739926_647533195 NZ_GG770509_647533119 81.82 22 4 0 992 1013 989 1010 1.5e+02 24.0
# BLAT 34 [2006/03/10]
# Query: NZ_ACIZ01000148_643886127
# Database: test_db.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_ACIZ01000148_643886127 NZ_ACIZ01000148_643886127 100.00 1373 0 0 1 1373 1 1373 0.0e+00 2165.0
NZ_ACIZ01000148_643886127 NZ_GG770509_647533119 85.49 634 92 0 337 970 336 969 4.5e-234 807.0
NZ_ACIZ01000148_643886127 NZ_GG770509_647533119 86.08 237 33 0 1137 1373 1135 1371 1.2e-77 287.0
NZ_ACIZ01000148_643886127 NZ_GG770509_647533119 83.12 154 26 0 977 1130 976 1129 2.2e-48 190.0
NZ_ACIZ01000148_643886127 NZ_GG739926_647533195 76.22 572 136 0 414 985 414 985 1.7e-158 556.0
NZ_ACIZ01000148_643886127 NZ_GG739926_647533195 76.80 181 42 0 1022 1202 1023 1203 6.4e-53 205.0
NZ_ACIZ01000148_643886127 NZ_GG739926_647533195 96.00 50 2 0 1207 1256 1209 1258 6.4e-14 75.0
NZ_ACIZ01000148_643886127 NZ_GG739926_647533195 88.68 53 6 0 1321 1373 1315 1367 1.6e-09 61.0
NZ_ACIZ01000148_643886127 NZ_GG739926_647533195 77.27 22 5 0 990 1011 992 1013 8.5e+02 22.0
""".splitlines()
assign_reads_prot_exp = """# BLAT 34x13 [2009/02/26]
# Query: NZ_GG770509_647533119_frame_1
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG770509_647533119_frame_1 NZ_GG770509_647533119 96.83 441 0 7 1 427 1 441 8.9e-254 872.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_GG770509_647533119_frame_2
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG770509_647533119_frame_2 NZ_ACIZ01000148_643886127 85.37 41 6 0 359 399 362 402 8.0e-13 72.0
NZ_GG770509_647533119_frame_2 NZ_ACIZ01000148_643886127 93.75 16 1 0 419 434 421 436 1.3e+00 31.0
NZ_GG770509_647533119_frame_2 NZ_GG739926_647533195 75.86 29 7 0 320 348 326 354 2.9e-04 43.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_GG770509_647533119_frame_3
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG770509_647533119_frame_3 NZ_ACIZ01000148_643886127 80.61 98 19 0 210 307 209 306 7.5e-39 158.0
NZ_GG770509_647533119_frame_3 NZ_ACIZ01000148_643886127 66.33 98 33 0 43 140 44 141 8.9e-27 118.0
NZ_GG770509_647533119_frame_3 NZ_ACIZ01000148_643886127 78.95 38 8 0 310 347 308 345 2.3e-08 57.0
NZ_GG770509_647533119_frame_3 NZ_ACIZ01000148_643886127 66.67 30 10 0 178 207 178 207 2.5e-01 33.0
NZ_GG770509_647533119_frame_3 NZ_GG739926_647533195 53.00 100 47 0 131 230 134 233 1.9e-18 90.0
NZ_GG770509_647533119_frame_3 NZ_GG739926_647533195 68.89 45 14 0 238 282 241 285 5.9e-09 59.0
NZ_GG770509_647533119_frame_3 NZ_GG739926_647533195 72.09 43 12 0 63 105 66 108 3.0e-08 56.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_GG739926_647533195_frame_1
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG739926_647533195_frame_1 NZ_GG739926_647533195 100.00 437 0 0 1 437 1 437 1.7e-263 904.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 69.86 73 22 0 213 285 209 281 1.1e-20 98.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 53.33 60 28 0 148 207 145 204 1.3e-06 51.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 60.53 38 15 0 66 103 64 101 1.9e-03 41.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 76.92 26 6 0 2 27 3 28 9.7e-03 38.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 69.57 23 7 0 288 310 285 307 4.8e+00 29.0
NZ_GG739926_647533195_frame_1 NZ_ACIZ01000148_643886127 90.00 10 1 0 134 143 132 141 1.6e+04 18.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_GG739926_647533195_frame_2
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG739926_647533195_frame_2 NZ_GG770509_647533119 66.67 42 14 0 270 311 276 317 2.3e-08 57.0
NZ_GG739926_647533195_frame_2 NZ_GG770509_647533119 60.00 45 18 0 185 229 188 232 3.9e-06 49.0
NZ_GG739926_647533195_frame_2 NZ_GG770509_647533119 80.00 20 4 0 247 266 251 270 5.6e-01 32.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_GG739926_647533195_frame_3
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_GG739926_647533195_frame_3 NZ_ACIZ01000148_643886127 94.44 18 1 0 390 407 385 402 4.3e-03 39.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_ACIZ01000148_643886127_frame_1
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_ACIZ01000148_643886127_frame_1 NZ_ACIZ01000148_643886127 100.00 436 0 0 1 436 1 436 2.1e-261 897.0
NZ_ACIZ01000148_643886127_frame_1 NZ_GG739926_647533195 78.57 42 9 0 240 281 244 285 4.0e-10 63.0
NZ_ACIZ01000148_643886127_frame_1 NZ_GG739926_647533195 60.53 38 15 0 64 101 66 103 1.9e-03 41.0
NZ_ACIZ01000148_643886127_frame_1 NZ_GG739926_647533195 76.92 26 6 0 3 28 2 27 9.7e-03 38.0
NZ_ACIZ01000148_643886127_frame_1 NZ_GG739926_647533195 69.57 23 7 0 285 307 288 310 4.8e+00 29.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_ACIZ01000148_643886127_frame_2
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_ACIZ01000148_643886127_frame_2 NZ_GG770509_647533119 79.59 147 26 2 182 324 189 335 2.3e-61 233.0
NZ_ACIZ01000148_643886127_frame_2 NZ_GG770509_647533119 72.73 33 9 0 128 160 137 169 5.0e-04 42.0
NZ_ACIZ01000148_643886127_frame_2 NZ_GG770509_647533119 90.91 22 2 0 70 91 76 97 2.5e-03 40.0
# BLAT 34x13 [2009/02/26]
# Query: NZ_ACIZ01000148_643886127_frame_3
# Database: /home/adro2179/metagenome/test_db_prot.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
NZ_ACIZ01000148_643886127_frame_3 NZ_GG770509_647533119 84.21 38 4 1 360 395 367 404 3.0e-08 56.0
NZ_ACIZ01000148_643886127_frame_3 NZ_GG770509_647533119 94.12 17 1 0 413 429 425 441 1.6e+00 31.0
NZ_ACIZ01000148_643886127_frame_3 NZ_GG739926_647533195 78.57 28 5 1 321 347 326 353 1.5e-03 41.0"""
assign_reads_prot_exp = assign_reads_prot_exp.splitlines()
test_db_prot = """>NZ_GG770509_647533119
YLEFDPGSERTLAAGLTHASRASGRRVSNAWERTICYGITQGNLCYRMetWKVGKSARVGLASWWGKGSPRRRSIAGLRGSATLGLRHGPDSYGRQQWGILDNGRKPDPAMetPRERPGCKALSPVKMetTVTGEEAPANFVPAAAVIRRGLALFGFTGRKAHVGGLLSQGNPGAQPRNCLYWKSVWRVEFRVRNSIFGGTPVAKAAHWTNRGAKAWGANRIRYPGSPRRKRMetLAVGASVAQLTHTFRLGSAVARLKLKGIDGGPHKRWSMetWFNSKQRAEPYQPLTSTGAAWLSSARVVRCWVKSRNERNPRPLPAWALGDCRAGGRWGRQVLMetALTGWATHVLQWWSVGSEHASVSSPPSQFGCTLQLECRSWNRSRISMetPRIRSRALYTPPVTPWELVLPEGACAGDHGRVSDWGEVVTRPGNLRLDHLLS
>NZ_GG739926_647533195
WEFDPGSGTLATGLTHASRGTGARVSNAYPTFPRPRDNLPKGRLIPYVQSRSRMGMRPISLLAGQRPTKASIGRGSERKAPHTGTETRSRLLREAAVRNIGQWAEATSQVACRTTAYGLTAFMRGYAGTAIRTGFRASSRGNTEGPGVIRIYWVRERRPPCKRAVKSSGPTAALRRELLGLSAPEAGGIRGVAVKCLDITKNPDCEGSPLWRLTLRLEGAGIEQDIPWSARTMDTRCPALGGQAKALSIPPGEYAGNGETQRNRGPAQAEEHVVFDDTRGTLPGLELRCCMVVVSSCREVSAQVPRAQPLSAVAIGRALCGHCRRKVEEGGDDVKSARPLRPGPHTCYNGRQRAVRAQVRVNPLRSQFGWGLQPDPRSWIRSRISHGAVNTFPGLVHTARQAMKAGGASPCRPRAKPVIGAKSQGSRTGRCGWNTSF
>NZ_ACIZ01000148_643886127
NMEFDPGSGTLAACLIHASRTSGGRVSNTWVTCPVGDNIWKQMLIPHKESRFWMDPRRISLVRRLTKAMIRSRTERLIGHIGTETRPKLLREAAVGNLPQWTQVWSNAAVKKAFGSNSVVGEDDGIQPESHGLRASSRGNTVASVIRIYWASERRRFFKSDVKALGLTEEVHRKLGNLSAEEDSGTPCVAVKCVDIWKNTSGEGGCLVLTLRLESMGSEQDIPWSMPTMNARCWSFSAAANALSIPPGEYDRKVETQRNRGPAQAVEHVVFEATRRTLPGLDIDRWCMVVVSSCREMLGVPQRAQPLLVASMGTLVRLPVTNRRKVGMTSNHHAPYDLGYTRATMDGNELRDREVKLISSILSSDVGCNSPTEVGIASNRGSARRGEYVPGPCTHRPSHHESLHPKPVRSEPSKVGQMIRVKSQGSRRRTCGWITS"""
test_db_prot = test_db_prot.splitlines()
test_db_dna = """>NZ_GG770509_647533119
UACUUGGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCAUUUGCUACGGAAUAACUCAGGGAAACUUGUGCUAAUACCGUAUGUGGAAAGUCGGCAAAUGAUCGGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCUCACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUCACCGGUGAAGAUGACGGUAACCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAUUUACUGGGCGUAAAGCGCACGUAGGCGGACUUUUAAGUCAGGGGUGAAAUCCCGGGGCUCAACCCCGGAACUGCCUUUGAUACUGGAAGUCUUGAGUAUGGUAGAGGUGAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACACCAGUGGCGAAGGCGGCUCACUGGACCAACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGGCUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUGCGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCCCUUGACAUCGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUCAGUGGGCAGCGAGCACGCGAGUGUGAGCUAAUCUCCGCCAUCUCAGUUCGGAUGCACUCUGCAACUCGAGUGCAGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGCGCUUGCUAGGCAGGCGACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU
>NZ_GG739926_647533195
UAAUGGGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCUACAGGCUUAACACAUGCAAGUCGAGGGACCGGCGCACGGGUGAGUAACGCGUAUCCAACCUUCCCGCGACCAAGGGAUAACCUGCCGAAAGGCAGACUAAUACCUUAUGUCCAAAGUCGGUCACGGAUGGGGAUGCGUCCGAUUAGCUUGUUGGCGGGGCAACGGCCCACCAAGGCAUCGAUCGGUAGGGGUUCUGAGAGGAAGGCCCCCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGGCGGAAGCCUGAACCAGCCAAGUAGCGUGCAGGACGACGGCCUACGGGUUGUAAACUGCUUUUAUGCGGGGAUAUGCAGGUACCGCAUGAAUAAGGACCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGAAGGUCCGGGCGUUAUCCGGAUUUAUUGGGUUUAAAGGGAGCGCAGGCCGCCGUGCAAGCGUGCCGUGAAAAGCAGCGGCCCAACCGCUGCCCUGCGGCGCGAACUGCUUGGCUUGAGUGCGCCGGAAGCGGGCGGAAUUCGUGGUGUAGCGGUGAAAUGCUUAGAUAUCACGAAGAACCCCGAUUGCGAAGGCAGCCCGCUGUGGCGACUGACGCUGAGGCUCGAAGGUGCGGGUAUCGAACAGGAUUAGAUACCCUGGUAGUCCGCACGGUAAACGAUGGAUACCCGCUGUCCGGCUCUGGGCGGCCAAGCGAAAGCGUUAAGUAUCCCACCUGGGGAGUACGCCGGCAACGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGCUUGAAUUGUGAAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUCAAGUGCCAUAACGAGCGCAACCCCUCUCCGCAGUUGCCAUCGGCCGGGCACUCUGCGGACACUGCCGCCGCAAGGUGGAGGAAGGUGGGGAUGACGUCAAAUCAGCACGGCCCUUACGUCCGGGGCCACACACGUGUUACAAUGGCCGGCAGAGGGCUGUCCGCGCGCAAGUGCGGGUGAAUCCCCUCCGGUCCCAGUUCGGAUGGGGUCUGCAACCCGACCCCAGAAGCUGGAUUCGCUAGUAAUCGCGCAUCAGCCAUGGCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGAAAGCCGGGGGUGCCUGAAGUCCGUGUCGGCCUAGGGCAAAACCGGUGAUUGGGGCUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAACACCUCCUUUCU
>NZ_ACIZ01000148_643886127
AAUAUGGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAACGAGUGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUUAAGUGGGGGAUAACAUUUGGAAACAGAUGCUAAUACCGCAUAAAGAAAGUCGCUUUUGGAUGGACCCGCGGCGUAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAAUGAUACGUAGCCGAACUGAGAGGUUGAUCGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGACGCAAGUCUGAUGGAGCAACGCCGCGUGAGUGAAGAAGGCUUUCGGGUCGUAAAACUCUGUUGUUGGAGAAGAUGACGGUAUCCAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCGAGCGCAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCUCGGCUUAACCGAGGAAGUGCAUCGGAAACUGGGAAACUUGAGUGCAGAAGAGGACAGUGGAACUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGUGGCGAAGGCGGCUGUCUGGUCUGACUGACGCUGAGGCUCGAAAGCAUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAAUGCUAGGUGUUGGAGCUUCAGUGCCGCAGCUAACGCAUUAAGCAUUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUGACUAGUUGCCAGCAUGGGCACUCUAGUAAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGAUGGCAACGAGUUGCGAGACCGCGAGGUCAAGCUAAUCUCUUCCAUUCUCAGUUCGGAUGUAGGCUGCAACUCGCCUACAGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCACGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGUUUGUAACACCCGAAGCCGGUGCGUAGCGAGCCGUCUAAGGUGGGACAAAUGAUUAGGGUGAAGUCGUAACAAGGUAGCCGUAGGAGAACCUGCGGCUGGAUCACCUCCUUUCU"""
test_db_dna = test_db_dna.splitlines()
test_query = """>NZ_GG770509_647533119
UACUUGGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCAUUUGCUACGGAAUAACUCAGGGAAACUUGUGCUAAUACCGUAUGUGGAAAGUCGGCAAAUGAUCGGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCUCACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUCACCGGUGAAGAUGACGGUAACCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAUUUACUGGGCGUAAAGCGCACGUAGGCGGACUUUUAAGUCAGGGGUGAAAUCCCGGGGCUCAACCCCGGAACUGCCUUUGAUACUGGAAGUCUUGAGUAUGGUAGAGGUGAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACACCAGUGGCGAAGGCGGCUCACUGGACCAACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGGCUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUGCGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCCCUUGACAUCGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUCAGUGGGCAGCGAGCACGCGAGUGUGAGCUAAUCUCCGCCAUCUCAGUUCGGAUGCACUCUGCAACUCGAGUGCAGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGCGCUUGCUAGGCAGGCGACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU
>NZ_GG739926_647533195
UAAUGGGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCUACAGGCUUAACACAUGCAAGUCGAGGGACCGGCGCACGGGUGAGUAACGCGUAUCCAACCUUCCCGCGACCAAGGGAUAACCUGCCGAAAGGCAGACUAAUACCUUAUGUCCAAAGUCGGUCACGGAUGGGGAUGCGUCCGAUUAGCUUGUUGGCGGGGCAACGGCCCACCAAGGCAUCGAUCGGUAGGGGUUCUGAGAGGAAGGCCCCCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGGCGGAAGCCUGAACCAGCCAAGUAGCGUGCAGGACGACGGCCUACGGGUUGUAAACUGCUUUUAUGCGGGGAUAUGCAGGUACCGCAUGAAUAAGGACCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGAAGGUCCGGGCGUUAUCCGGAUUUAUUGGGUUUAAAGGGAGCGCAGGCCGCCGUGCAAGCGUGCCGUGAAAAGCAGCGGCCCAACCGCUGCCCUGCGGCGCGAACUGCUUGGCUUGAGUGCGCCGGAAGCGGGCGGAAUUCGUGGUGUAGCGGUGAAAUGCUUAGAUAUCACGAAGAACCCCGAUUGCGAAGGCAGCCCGCUGUGGCGACUGACGCUGAGGCUCGAAGGUGCGGGUAUCGAACAGGAUUAGAUACCCUGGUAGUCCGCACGGUAAACGAUGGAUACCCGCUGUCCGGCUCUGGGCGGCCAAGCGAAAGCGUUAAGUAUCCCACCUGGGGAGUACGCCGGCAACGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGCUUGAAUUGUGAAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUCAAGUGCCAUAACGAGCGCAACCCCUCUCCGCAGUUGCCAUCGGCCGGGCACUCUGCGGACACUGCCGCCGCAAGGUGGAGGAAGGUGGGGAUGACGUCAAAUCAGCACGGCCCUUACGUCCGGGGCCACACACGUGUUACAAUGGCCGGCAGAGGGCUGUCCGCGCGCAAGUGCGGGUGAAUCCCCUCCGGUCCCAGUUCGGAUGGGGUCUGCAACCCGACCCCAGAAGCUGGAUUCGCUAGUAAUCGCGCAUCAGCCAUGGCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGAAAGCCGGGGGUGCCUGAAGUCCGUGUCGGCCUAGGGCAAAACCGGUGAUUGGGGCUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAACACCUCCUUUCU
>NZ_ACIZ01000148_643886127
AAUAUGGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAACGAGUGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUUAAGUGGGGGAUAACAUUUGGAAACAGAUGCUAAUACCGCAUAAAGAAAGUCGCUUUUGGAUGGACCCGCGGCGUAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAAUGAUACGUAGCCGAACUGAGAGGUUGAUCGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGACGCAAGUCUGAUGGAGCAACGCCGCGUGAGUGAAGAAGGCUUUCGGGUCGUAAAACUCUGUUGUUGGAGAAGAUGACGGUAUCCAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCGAGCGCAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCUCGGCUUAACCGAGGAAGUGCAUCGGAAACUGGGAAACUUGAGUGCAGAAGAGGACAGUGGAACUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGUGGCGAAGGCGGCUGUCUGGUCUGACUGACGCUGAGGCUCGAAAGCAUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAAUGCUAGGUGUUGGAGCUUCAGUGCCGCAGCUAACGCAUUAAGCAUUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUGACUAGUUGCCAGCAUGGGCACUCUAGUAAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGAUGGCAACGAGUUGCGAGACCGCGAGGUCAAGCUAAUCUCUUCCAUUCUCAGUUCGGAUGUAGGCUGCAACUCGCCUACAGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCACGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGUUUGUAACACCCGAAGCCGGUGCGUAGCGAGCCGUCUAAGGUGGGACAAAUGAUUAGGGUGAAGUCGUAACAAGGUAGCCGUAGGAGAACCUGCGGCUGGAUCACCUCCUUUCU"""
test_query = test_query.splitlines()
if __name__ == '__main__':
main()
|
