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#!/usr/bin/env python
from string import split, strip
from os import popen, remove
from glob import glob
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import QMEBlast9
from cogent.app.blast import seqs_to_stream,\
make_subject_match_scorer, make_shotgun_scorer, keep_everything_scorer, \
ids_from_seq_lower_threshold, PsiBlast, psiblast_n_neighbors
__author__ = "Micah Hamady"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Micah Hamady", "Rob Knight", "Catherine Lozupone"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Micah Hamady"
__email__ = "hamady@colorado.edu"
__status__ = "Prototype"
class BlastTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""Define some standard data"""
self.rec = """# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 1
# Query: ece:Z4181
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4181 ece:Z4181 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-06 52.8
# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 2
# Query: ece:Z4181
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4181 ece:Z4181 100.00 110 0 0 1 110 1 110 3e-54 211
ece:Z4181 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-54 211
ece:Z4181 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-08 59.0
ece:Z4181 sfl:CP0138 33.98 103 57 2 8 110 6 97 6e-06 50.5
ece:Z4181 spt:SPA2730 37.50 72 45 0 39 110 30 101 1e-05 49.8
ece:Z4181 sec:SC2804 37.50 72 45 0 39 110 30 101 1e-05 49.8
ece:Z4181 stm:STM2872 37.50 72 45 0 39 110 30 101 1e-05 49.8
# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 1
# Query: ece:Z4182
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4182 ece:Z4182 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4182 ecs:ECs3718 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4182 cvi:CV2422 41.67 72 42 0 39 110 29 100 2e-06 52.8""".split('\n')
self.rec2 = """# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 1
# Query: ece:Z4181
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4181 ece:Z4181 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 spt:SPA2730 37.50 72 45 0 39 110 30 101 1e-05 49.8
# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 2
# Query: ece:Z4181
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4181 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-54 211
ece:Z4181 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-08 59.0
# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 1
# Query: ece:Z4182
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4182 ece:Z4182 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4182 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-06 52.8""".split('\n')
self.rec3 = """# BLASTP 2.2.10 [Oct-19-2004]
# BLASTP 2.2.10 [Oct-19-2004]
# Query: ece:Z4181
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4181 ece:Z4182 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4181 spt:SPA2730 37.50 72 45 0 39 110 30 101 1e-05 49.8
# BLASTP 2.2.10 [Oct-19-2004]
# Iteration: 1
# Query: ece:Z4182
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4182 ece:Z4182 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4182 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-06 52.8
# BLASTP 2.2.10 [Oct-19-2004]
# Query: ece:Z4183
# Database: db/everything.faa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
ece:Z4183 ece:Z4182 100.00 110 0 0 1 110 1 110 3e-47 187
ece:Z4183 ecs:ECs3717 100.00 110 0 0 1 110 1 110 3e-54 211
ece:Z4183 cvi:CV2421 41.67 72 42 0 39 110 29 100 2e-08 59.0""".split('\n')
self.query_1 = """>gi|100002553| Bd2556c Bd2556c two-component system sensor histidine kinase 3092017:3094158 reverse MW:81963
MRLKNRLNNWISIRMGMVIVIFLGVSCGSMRSSTPPPAKDRLTEIDSLERLLPDCPTIASTLPLLRRLAFLYQQQSEMKVYNERLYENAMAVDSISVAYLGLKNLAEYYYDQSVRDSLEYYCSLVDSIAKARHEYPNVLFDVKSLSSQDLLWLGNYELAMSEAMDLYRLASNLDHRYGLLRCSETLGLIYQRIRRDSDAVVSFQESLDLLKDIKDVPDIMDTKVRLTSYQLESSVRTKQYASTERILGQYMALLDEQYKIYQEKNDLLSIKREYWLLYSFYTSFYLSQGDLENAKRSLDQASSYADSNWVEGDYAINTYLTVKARYHKAAGDIPLALHCINEVLETERLPEDIQFKADILKEQGQLGEVMALYDELYSTLTKRRGTSFLRQVNQLRTLHELHEKELKETELKEAGQRIARKQDLLIFILSISVVLLILLYVLFLYYRHLRSLKNQLQREKELLLESQRQLIKEKTRAEEASLMKSAFLANMSHEVRTPLNAIVGFSGLLVEPSTDEEERKEYSSIIRNNTDLMLNLVNDVLDLSRMETGDLHFDIKDHLLLVCCQMALESVRHRIPDGVKLTFSPAGEPIVVHVDNLRLQQLLTNLLTNAAKFTEKGEINLSFQLEPDRKKVCIAVTDTGAGIPLEKQATIFNRFEKLDDYKPGVGLGLSICLLIAERLDGALFIDSSYTDGARFVLILSCEIDSSIYNPPIEV"""
self.query_2 = """>gi|100002557| Bd2560c Bd2560c conserved hypothetical protein 3097971:3098210 reverse MW:8927
MGKNQLIHGNEFHLLKQAEIHKATGKLVESLNLAAGSTGGFDIYKVVEAYFTDLEKRKEINDLLGISEPCETRVTEECFS
"""
self.fasta_recs = """>gi|100002550| Bd2553c Bd2553c conserved hypothetical protein 3090609:3091013 reverse MW:14682
MMDFISVPLVVGIVCAGIYGLFELFVRKRERLAIIEKIGDKLDTSAFDGKLGLPNYMRNFSFSSLKAGCLLAGIGLGLLVGFIINMCMATNSYYDDGWYRHEVAGTAYGASVLLFGGIGLIIAFVIELKLGKNNK
>gi|100002551| Bd2554 Bd2554 RNA polymerase ECF-type sigma factor 3091112:3091717 forward MW:23408
LLPQVVTYLPGLRPLSTMELYTDTYYIQRIQAGDVACFACLLDKYSRPIHSLILKVVRSQEEAEELAQDTFMKVFKNLASFKGDCSFSTWIYRIAYNTAISSVRKKRYEFLAIEETTLENVSEEEITNLFGQTESTEQVQRLEVALEQLLPDERALILLFYWKEKTIEELVSITGLTASNIKVKLHRIRKKLFVLLNGMDHE
>gi|100002552| Bd2555 Bd2555 conserved hypothetical protein 3091713:3092066 forward MW:13332
MSKINTNKEQPDLLGDLFKRIPEEELPASFRSNVMRQIMLESAKAKKRDERFSLLAAIVASLIMISLAIVSFVYMEIPKIAIPTISTSALAFYLYIGAITLILLLADYKLRNLFHKKG
>gi|100002553| Bd2556c Bd2556c two-component system sensor histidine kinase 3092017:3094158 reverse MW:81963
MRLKNRLNNWISIRMGMVIVIFLGVSCGSMRSSTPPPAKDRLTEIDSLERLLPDCPTIASTLPLLRRLAFLYQQQSEMKVYNERLYENAMAVDSISVAYLGLKNLAEYYYDQSVRDSLEYYCSLVDSIAKARHEYPNVLFDVKSLSSQDLLWLGNYELAMSEAMDLYRLASNLDHRYGLLRCSETLGLIYQRIRRDSDAVVSFQESLDLLKDIKDVPDIMDTKVRLTSYQLESSVRTKQYASTERILGQYMALLDEQYKIYQEKNDLLSIKREYWLLYSFYTSFYLSQGDLENAKRSLDQASSYADSNWVEGDYAINTYLTVKARYHKAAGDIPLALHCINEVLETERLPEDIQFKADILKEQGQLGEVMALYDELYSTLTKRRGTSFLRQVNQLRTLHELHEKELKETELKEAGQRIARKQDLLIFILSISVVLLILLYVLFLYYRHLRSLKNQLQREKELLLESQRQLIKEKTRAEEASLMKSAFLANMSHEVRTPLNAIVGFSGLLVEPSTDEEERKEYSSIIRNNTDLMLNLVNDVLDLSRMETGDLHFDIKDHLLLVCCQMALESVRHRIPDGVKLTFSPAGEPIVVHVDNLRLQQLLTNLLTNAAKFTEKGEINLSFQLEPDRKKVCIAVTDTGAGIPLEKQATIFNRFEKLDDYKPGVGLGLSICLLIAERLDGALFIDSSYTDGARFVLILSCEIDSSIYNPPIEV
>gi|100002554| Bd2557c Bd2557c two-component system sensor histidine kinase 3094158:3095507 reverse MW:51247
LERKYNGEGKIFPVKRHRCLMSCYYCELYTMKGNSGKAQAYLDQATAYLDSSFGDRVEAQYLRTKSFYYWKEKDYRHALSAVNLALKINRDLDKLEMKKAVLQSSGQLQEAVTIYEEIINKTETINTDAFDRQIEQLRVLNDLNDLEKQDRELKLKSEQEALKQKQIVVSIGLLLVLMGLLYMLWRIYMHTKRLRNELLQEKDSLTASEKQLRVVTKEAEAANKKKSAFIANISHEVRTPLNAIVGFSELLASSEYSEEEKIRFAGEVNHSSELLLNLVNDVLDLSRLESGKIKFSVKPNDLVACCQRALDSIRHRVKPGVRLTFTPSIESYTLNTDALRLQQLLTNLLSNAAKFTSEGEINLSFTVDEGKEEVCFSVTDTGCGIPEDKCEKIFERFEKLDDFIQGTGLGLSVCQIISEQLNGSLSVDISYKDGARFVFIHPTNLIETPI
>gi|100002555| Bd2558c Bd2558c hypothetical protein 3095527:3095985 reverse MW:17134
LRGKNIHLGRVGCNYGKLLIFIDIYFVSLRIVSDKSMSRGFLRKSSVNTFIGIVWILFAVGTSAQNAVSKFRADSIRQSLSRIQKPQDKIPLLKELIGLYWQLPEEVLALKEIIDIAMPLDSIGIVYDAMAGLSRYYPAIRTFVRVGGALETV
>gi|100002556| Bd2559 Bd2559 30S ribosomal protein S1 3096095:3097882 forward MW:67092
MENLKNIQPVEDFNWDAFEQGETYTEVSKDDLVKTYDETLNTVKDKEVVMGTVTSMNKREVVVNIGFKSDGVVPMSEFRYNPDLKIGDEVEVYIESQEDKKGQLILSHKKARATRSWDRVNEALEKDEIIKGYIKCRTKGGMIVDVFGIEAFLPGSQIDVKPIRDYDVFVGKTMEFKIVKINQEFKNVVVSHKALIEAELEQQKKDIISKLEKGQVLEGTVKNITSYGVFIDLGGVDGLIHITDLSWGRVSHPEEIVQLDQKINVVILDFDDEKKRIALGLKQLTPHPWDALDTNLKVGDKVKGKVVVMADYGAFIEIAPGVEGLIHVSEMSWTQHLRSAQDFMKVGDEIEAVILTLDRDERKMSLGIKQLKADPWENIEERFPVGSRHAAKVRNFTNFGVFVEIEEGVDGLIHISDLSWTKKIKHPSEFTQIGAEIEVQVLEIDKENRRLSLGHKQLEENPWDVFETIFTVGSIHEGTIIEVLDKGAVISLPYGVEGFATPKHLVKEDGSQAQVDEKLSFKVIEFNKEAKRIILSHSRIFEDEQKGAKATSEKKASSKRGGKKEEESGMVTGPVEKTTLGDIEELAALKEKLSGK
>gi|100002557| Bd2560c Bd2560c conserved hypothetical protein 3097971:3098210 reverse MW:8927
MGKNQLIHGNEFHLLKQAEIHKATGKLVESLNLAAGSTGGFDIYKVVEAYFTDLEKRKEINDLLGISEPCETRVTEECFS
>gi|100002558| Bd2561 Bd2561 phosphoglycolate phosphatase 3098389:3099033 forward MW:24182
MKKLVIFDLDGTLLNTIADLAHSTNHALRQNGFPTHDVKEYNFFVGNGINKLFERALPEGEKTAENILKVREEFLKHYDLHNTDRSVPYPGVPELLALLQERGIKLAVASNKYQAATRKLIAHFFPSIQFTEVLGQREGVKAKPDPSIVNEIVERASISKESTLYVGDSDVDMQTAINSEVTSCGVTWGFRPRTELEKYAPDHIAEKAEDILKFI
>gi|100002559| Bd2562 Bd2562 conserved hypothetical protein 3099382:3100299 forward MW:35872
MSGNIKKIVEPNSGIDYSLEKDFKIFTLSKELPITTYPSYIRLGIVIYCVKGNAKIDIYSNKHIITPKELIIILPGQLVALTDVSVDFQIRYFTITESFYSDILSGISRFSPHFFFYMRQHYYFKMEDVETLSFVDFFELLIRKAVDPENQYRRESVILLLRILFLDIYNHYKVNSLDSTATIDVHKKELTHKFFQLVMSNYKVNRSVTFYANSLCITPKYLTMVVKEVSGKSAKDWITEYMILELKGLLTNSTLNIQEIVEKTQFSNQSSLGRFFRRHTGLSPLQYRKKYLTTEQRTNFSKNNTI
"""
def test_seqs_to_stream(self):
"""seqs_to_stream should iterate over seqs"""
sts = seqs_to_stream
self.assertEqual(list(sts('>a\nTG\n>b\nWW\n', \
'_input_as_multiline_string')),\
[['>a','TG'],['>b','WW']])
#skipping test for file open
self.assertEqual(list(sts(['TG','WW'], '_input_as_seqs')), \
[['>0','TG'],['>1','WW']])
self.assertEqual(list(sts(['>a','TG','>b','WW'], \
'_input_as_lines')),\
[['>a','TG'],['>b','WW']])
self.assertRaises(TypeError, sts, 'abc', 'xyz')
def test_make_subject_match_scorer(self):
"""make_subject_match_scorer should keep ids matching n queries"""
qm1 = make_subject_match_scorer(1)
qm3 = make_subject_match_scorer(3)
qm5 = make_subject_match_scorer(5)
qmes = wrap_qmes(QMEBlast9(self.rec3))
self.assertEqualItems(qm1(qmes), ['ece:Z4181','ece:Z4182','ece:Z4183'])
self.assertEqualItems(qm3(qmes), ['ece:Z4181','ece:Z4183'])
self.assertEqualItems(qm5(qmes), [])
def test_make_shotgun_scorer(self):
"""make_shotgun_scorer should keep ids matching n queries"""
sg1 = make_shotgun_scorer(1)
sg2 = make_shotgun_scorer(2)
sg3 = make_shotgun_scorer(3)
sg4 = make_shotgun_scorer(4)
sg5 = make_shotgun_scorer(5)
qmes = wrap_qmes(QMEBlast9(self.rec3))
self.assertEqualItems(sg1(qmes), keep_everything_scorer(qmes))
self.assertEqualItems(sg2(qmes), \
['ece:Z4181','ece:Z4182','ece:Z4183','cvi:CV2421','ecs:ECs3717'])
self.assertEqualItems(sg3(qmes), \
['ece:Z4181','ece:Z4182','ece:Z4183'])
self.assertEqualItems(sg4(qmes), \
['ece:Z4182'])
self.assertEqualItems(sg5(qmes), [])
def test_keep_everything_scorer(self):
"""keep_everything_scorer should keep all ids found."""
k = keep_everything_scorer(wrap_qmes(QMEBlast9(self.rec2)))
self.assertEqualItems(k, \
['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])
def test_ids_from_seq_lower_threshold(self):
"ids_from_seq_lower_threshold returns psiblast hits, decreasing sens"
bdb_seqs = self.fasta_recs
f = open('test_bdb', 'w')
f.write(bdb_seqs)
f.close()
temp = popen('formatdb -i test_bdb -o T -p T')
params = {'-j':2,
'-d':'test_bdb'}
query = self.query_1.split('\n')
app = PsiBlast(params=params,
InputHandler='_input_as_lines')
#the command below should result in finding itself and 2554
#it should run for max_iterations
result = ids_from_seq_lower_threshold(query, n=12, \
max_iterations=4, app=app, core_threshold=1e-50, \
lower_threshold=1e-20, step=10000)
self.assertEqual(result[0],\
[('gi|100002553', '0.0'), ('gi|100002554', '0.0')])
self.assertEqual(result[1], 4)
#if n=2, it should find the same sequences but only run for 1 iteration
#since it would hit n after the first blast search
result = ids_from_seq_lower_threshold(query, n=2, \
max_iterations=4, app=app, core_threshold=1e-50, \
lower_threshold=1e-20, step=10000)
self.assertEqual(result[0],\
[('gi|100002553', '0.0'), ('gi|100002554', '0.0')])
self.assertEqual(result[1], 1)
query = self.query_2.split('\n')
#query_2_s e-value for itself is 9e-47, it should not be found
#with the lower_threshold set to 1e-48
result = ids_from_seq_lower_threshold(query, n=12, \
max_iterations=4, app=app, core_threshold=1e-50, \
lower_threshold=1e-48, step=10000)
self.assertEqual(result[0], [])
#it also should not be found if the max_iterations is set to 1
result = ids_from_seq_lower_threshold(query, n=12, \
max_iterations=1, app=app, core_threshold=1e-50, \
lower_threshold=1e-20, step=10000)
self.assertEqual(result[0], [])
for fname in ['formatdb.log'] + glob('test_bdb*'):
remove(fname)
def test_psiblast_n_neighbors(self):
"psiblast_n_neighbors psiblasts and stops when n neighbors are reached"
bdb_seqs = self.fasta_recs
f = open('test_bdb', 'w')
f.write(bdb_seqs)
f.close()
temp = popen('formatdb -i test_bdb -o T -p T')
params = {'-j':11}
lines = bdb_seqs.split('\n')
results = psiblast_n_neighbors(lines, n=12, blast_db='test_bdb', \
method='lower_threshold', params=params,\
core_threshold=1e-50, step=10000)
#there should be 10 result entries since there were 10 queries
self.assertEqual(len(results), 10)
for i in results:
#each query should at least find itself
self.failUnless(len(results[i][0]) >= 1)
#each query should iterate 8 times since it can never reach max
self.assertEqual(results[i][1], 11)
for fname in ['formatdb.log'] + glob('test_bdb*'):
remove(fname)
def wrap_qmes(qmes):
"""Converts qmes into a dict of {q:{m:e}}"""
d = {}
for q, m, e in qmes:
if q not in d:
d[q] = {}
d[q][m] = e
return d
if __name__ == "__main__":
main()
|
