1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188
|
#!/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 2007-2016, The Cogent Project"
__credits__ = ["Micah Hamady", "Rob Knight", "Catherine Lozupone"]
__license__ = "GPL"
__version__ = "1.9"
__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 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()
|