fixtures.py 22.04 KiB
"""
Test fixtures.
"""
from __future__ import unicode_literals
import os
import shutil
import pytest
import yaml
from mutalyzer.config import settings as _settings
from mutalyzer.output import Output
from mutalyzer.redisclient import client as redis
from mutalyzer.db.models import (Assembly, Chromosome, Reference,
TranscriptMapping)
from mutalyzer import db as _db
@pytest.fixture(autouse=True)
def settings(request, tmpdir):
cache_dir = unicode(tmpdir.mkdir('cache'))
log_file = unicode(tmpdir.join('log').ensure())
redis_uri = request.config.option.redis_uri
_settings.configure({
'DEBUG': False,
'TESTING': True,
'CACHE_DIR': cache_dir,
'LOG_FILE': log_file,
'DATABASE_URI': None,
'REDIS_URI': redis_uri
})
if redis_uri is not None:
redis.flushdb()
return _settings
@pytest.fixture
def output(settings):
return Output('test')
@pytest.fixture
def db(request, settings, database_uri):
settings.configure({
'DATABASE_URI': database_uri
})
# Mutalyzer create tables automatically if we're using an SQLite
# in-memory database.
if database_uri != 'sqlite://':
_db.Base.metadata.drop_all(_db.session.get_bind())
_db.Base.metadata.create_all(_db.session.get_bind())
request.addfinalizer(_db.session.remove)
return _db
@pytest.fixture(scope='session')
def available_references():
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'data', 'references.yml')
with open(filename) as f:
return yaml.safe_load(f)
def _add_links(settings, links):
"""
Add transcript-protein links to the cache.
"""
for transcript, protein in links:
if transcript is not None:
key = 'ncbi:transcript-to-protein:%s' % transcript
if protein is not None:
redis.set(key, protein)
if '.' in transcript:
key = key.rsplit('.', 1)[0]
redis.set(key, protein.rsplit('.', 1)[0])
else:
redis.setex(key,
settings.NEGATIVE_LINK_CACHE_EXPIRATION,
'')
if protein is not None:
key = 'ncbi:protein-to-transcript:%s' % protein
if transcript is not None:
redis.set(key, transcript)
if '.' in protein:
key = key.rsplit('.', 1)[0]
redis.set(key, transcript.rsplit('.', 1)[0])
else:
redis.setex(key,
settings.NEGATIVE_LINK_CACHE_EXPIRATION,
'')
@pytest.fixture
def references(request, settings, db, available_references):
try:
keys = request.param
except AttributeError:
return []
references = []
for key in keys:
entry = available_references[key]
try:
accession = entry['accession']
except KeyError:
accession = key
geninfo_id = entry.get('geninfo_id')
# TODO: use pytest basepath or something?
path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'data',
entry['filename'])
shutil.copy(path, settings.CACHE_DIR)
references.append(Reference(
accession, entry['checksum'], geninfo_identifier=geninfo_id))
_add_links(settings, entry.get('links', []))
db.session.add_all(references)
db.session.commit()
return references
@pytest.fixture
def links(request, settings, db, available_references):
try:
links = request.param
except AttributeError:
return []
_add_links(settings, links)
return links
@pytest.fixture
def hg19(db):
"""
Fixture for GRCh37/hg19 genome assembly with chromosomes.
"""
assembly = Assembly('GRCh37', 9606, 'Homo sapiens', alias='hg19')
db.session.add(assembly)
db.session.add_all(Chromosome(assembly, name, accession, organelle)
for accession, name, organelle in [
('NC_000001.10', 'chr1', 'nucleus'),
('NC_000002.11', 'chr2', 'nucleus'),
('NC_000003.11', 'chr3', 'nucleus'),
('NC_000004.11', 'chr4', 'nucleus'),
('NC_000005.9', 'chr5', 'nucleus'),
('NC_000006.11', 'chr6', 'nucleus'),
('NC_000007.13', 'chr7', 'nucleus'),
('NC_000008.10', 'chr8', 'nucleus'),
('NC_000009.11', 'chr9', 'nucleus'),
('NC_000010.10', 'chr10', 'nucleus'),
('NC_000011.9', 'chr11', 'nucleus'),
('NC_000012.11', 'chr12', 'nucleus'),
('NC_000013.10', 'chr13', 'nucleus'),
('NC_000014.8', 'chr14', 'nucleus'),
('NC_000015.9', 'chr15', 'nucleus'),
('NC_000016.9', 'chr16', 'nucleus'),
('NC_000017.10', 'chr17', 'nucleus'),
('NC_000018.9', 'chr18', 'nucleus'),
('NC_000019.9', 'chr19', 'nucleus'),
('NC_000020.10', 'chr20', 'nucleus'),
('NC_000021.8', 'chr21', 'nucleus'),
('NC_000022.10', 'chr22', 'nucleus'),
('NC_000023.10', 'chrX', 'nucleus'),
('NC_000024.9', 'chrY', 'nucleus'),
('NT_167244.1', 'chr6_apd_hap1', 'nucleus'),
('NT_113891.2', 'chr6_cox_hap2', 'nucleus'),
('NT_167245.1', 'chr6_dbb_hap3', 'nucleus'),
('NT_167246.1', 'chr6_mann_hap4', 'nucleus'),
('NT_167247.1', 'chr6_mcf_hap5', 'nucleus'),
('NT_167248.1', 'chr6_qbl_hap6', 'nucleus'),
('NT_167249.1', 'chr6_ssto_hap7', 'nucleus'),
('NT_167250.1', 'chr4_ctg9_hap1', 'nucleus'),
('NT_167251.1', 'chr17_ctg5_hap1', 'nucleus'),
('NC_012920.1', 'chrM', 'mitochondrion')])
db.session.commit()
return assembly
@pytest.fixture
def hg19_transcript_mappings(db, hg19):
"""
Fixture for some selected transcript mappings in the GRCh37/hg19 genome
assembly.
"""
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NM_003002',
'SDHD',
'forward',
111957571,
111966518,
[111957571, 111958581, 111959591, 111965529],
[111957683, 111958697, 111959735, 111966518],
'ncbi',
transcript=1,
cds=(111957632, 111965694),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NM_012459',
'TIMM8B',
'reverse',
111955524,
111957522,
[111955524, 111957364],
[111956186, 111957522],
'ncbi',
transcript=1,
cds=(111956019, 111957492),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NR_028383',
'TIMM8B',
'reverse',
111955524,
111957522,
[111955524, 111956702, 111957364],
[111956186, 111957034, 111957522],
'ncbi',
transcript=1,
cds=None,
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr6').one(),
'refseq',
'NM_000500',
'CYP21A2',
'forward',
32006082,
32009419,
[32006082, 32006499, 32006871, 32007133, 32007323, 32007526,
32007782, 32008183, 32008445, 32008646],
[32006401, 32006588, 32007025, 32007234, 32007424, 32007612,
32007982, 32008361, 32008548, 32009419],
'ncbi',
transcript=1,
cds=(32006200, 32008911),
select_transcript=False,
version=5))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr22').one(),
'refseq',
'NM_001145134',
'CPT1B',
'reverse',
51007290,
51017096,
[51007290, 51007765, 51008005, 51008722, 51009320, 51009587,
51009804, 51010435, 51010632, 51011304, 51011949, 51012764,
51012922, 51014464, 51014627, 51015286, 51015753, 51016204,
51016978],
[51007510, 51007850, 51008097, 51008835, 51009472, 51009721,
51009968, 51010551, 51010737, 51011489, 51012144, 51012848,
51013029, 51014541, 51014764, 51015463, 51015892, 51016363,
51017096],
'ncbi',
transcript=1,
cds=(51007767, 51016344),
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr22').one(),
'refseq',
'NR_021492',
'LOC100144603',
'forward',
51021455,
51022356,
[51021455, 51022027],
[51021752, 51022356],
'ncbi',
transcript=1,
cds=None,
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_001007553',
'CSDE1',
'reverse',
115259538,
115300624,
[115259538, 115261234, 115262200, 115263160, 115266504, 115267842,
115268832, 115269604, 115272879, 115273129, 115275225, 115276353,
115276610, 115277063, 115279379, 115280092, 115280584, 115282313,
115292442, 115300546],
[115260837, 115261366, 115262363, 115263338, 115266623, 115267954,
115269007, 115269711, 115273043, 115273269, 115275437, 115276478,
115276738, 115277144, 115279476, 115280184, 115280693, 115282511,
115292828, 115300624],
'ncbi',
transcript=1,
cds=(115260790, 115282511),
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_001130523',
'CSDE1',
'reverse',
115259538,
115300671,
[115259538, 115261234, 115262200, 115263160, 115266504, 115267842,
115268832, 115269604, 115272879, 115273129, 115275225, 115276353,
115276610, 115277063, 115279379, 115280584, 115282313, 115284148,
115292442, 115300546],
[115260837, 115261366, 115262363, 115263338, 115266623, 115267954,
115269007, 115269711, 115273043, 115273269, 115275437, 115276478,
115276738, 115277144, 115279476, 115280693, 115282511, 115284294,
115292828, 115300671],
'ncbi',
transcript=1,
cds=(115260790, 115284285),
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_002241',
'KCNJ10',
'reverse',
160007257,
160040051,
[160007257, 160039812],
[160012322, 160040051],
'ncbi',
transcript=1,
cds=(160011183, 160012322),
select_transcript=False,
version=4))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr20').one(),
'refseq',
'NM_001162505',
'TMEM189',
'reverse',
48740274,
48770335,
[48740274, 48744512, 48746083, 48747402, 48760039, 48770054],
[48741716, 48744724, 48746227, 48747484, 48760158, 48770335],
'ncbi',
transcript=1,
cds=(48741595, 48770174),
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr8').one(),
'refseq',
'NM_017780',
'CHD7',
'forward',
61591339,
61779465,
[61591339, 61653818, 61693559, 61707545, 61712947, 61714087,
61720776, 61728946, 61732566, 61734349, 61734583, 61735062,
61736399, 61741222, 61742881, 61748632, 61749376, 61750227,
61750635, 61754203, 61754406, 61757423, 61757809, 61761074,
61761610, 61763052, 61763591, 61763821, 61764578, 61765057,
61765388, 61766922, 61768534, 61769004, 61773463, 61774755,
61775107, 61777575],
[61591641, 61655656, 61693989, 61707686, 61713084, 61714152,
61720831, 61729060, 61732649, 61734486, 61734704, 61735305,
61736575, 61741365, 61743136, 61748842, 61749571, 61750394,
61750814, 61754313, 61754611, 61757622, 61757968, 61761163,
61761713, 61763181, 61763663, 61763878, 61764806, 61765265,
61766059, 61767082, 61768761, 61769447, 61773684, 61774895,
61775211, 61779465],
'ncbi',
transcript=1,
cds=(61653992, 61778492),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrM').one(),
'refseq',
'NC_012920',
'ND4',
'forward',
10760,
12137,
[10760],
[12137],
'reference',
transcript=1,
cds=(10760, 12137),
select_transcript=True,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_002001',
'FCER1A',
'forward',
159259504,
159278014,
[159259504, 159272096, 159272644, 159273718, 159275778, 159277538],
[159259543, 159272209, 159272664, 159273972, 159276035, 159278014],
'ncbi',
transcript=1,
cds=(159272155, 159277722),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr7').one(),
'refseq',
'XM_001715131',
'LOC100132858',
'reverse',
19828,
36378,
[19828, 20834, 31060, 32957, 35335, 36224],
[19895, 21029, 31437, 33107, 35541, 36378],
'ncbi',
transcript=1,
cds=(19828, 36378),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004011',
'DMD',
'reverse',
31137345,
32430371,
[31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
32408188, 32429869, 32430279],
[31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
32408298, 32430030, 32430371],
'ncbi',
transcript=1,
cds=(31140036, 32430326),
select_transcript=False,
version=3))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004019',
'DMD',
'reverse',
31196312,
31285024,
[31196312, 31198487, 31200855, 31222078, 31224699, 31227615,
31241164, 31279072, 31284927],
[31196922, 31198598, 31201021, 31222235, 31224784, 31227816,
31241238, 31279133, 31285024],
'ncbi',
transcript=1,
cds=(31196782, 31284946),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004007',
'DMD',
'reverse',
31137345,
33038317,
[31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
32408188, 32429869, 32456358, 32459297, 32466573, 32472779,
32481556, 32482703, 32486615, 32490281, 32503036, 32509394,
32519872, 32536125, 32563276, 32583819, 32591647, 32591862,
32613874, 32632420, 32662249, 32663081, 32715987, 32717229,
32827610, 32834585, 32841412, 32862900, 32867845, 33038256],
[31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
32408298, 32430030, 32456507, 32459431, 32466755, 32472949,
32481711, 32482816, 32486827, 32490426, 32503216, 32509635,
32519959, 32536248, 32563451, 32583998, 32591754, 32591963,
32613993, 32632570, 32662430, 32663269, 32716115, 32717410,
32827728, 32834757, 32841504, 32862977, 32867937, 33038317],
'ncbi',
transcript=1,
cds=(31140036, 32834745),
select_transcript=False,
version=2))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_203473',
'PORCN',
'forward',
48367371,
48379202,
[48367371, 48368172, 48369683, 48370280, 48370714, 48370977,
48371223, 48372628, 48372913, 48374105, 48374278, 48374449,
48375571, 48378763],
[48367491, 48368344, 48369875, 48370323, 48370895, 48371107,
48371240, 48372753, 48373013, 48374181, 48374341, 48374534,
48375681, 48379202],
'ncbi',
transcript=1,
cds=(48368209, 48378864),
select_transcript=False,
version=1))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_000132',
'F8',
'reverse',
154064063,
154250998,
[154064063, 154088707, 154089993, 154091358, 154124352, 154128141,
154129646, 154130326, 154132181, 154132571, 154133086, 154134695,
154156846, 154175973, 154182167, 154185232, 154189350, 154194245,
154194701, 154197606, 154212962, 154215512, 154221211, 154225248,
154227754, 154250685],
[154066027, 154088883, 154090141, 154091502, 154124507, 154128226,
154129717, 154130442, 154132363, 154132799, 154133298, 154134848,
154159951, 154176182, 154182317, 154185446, 154189443, 154194416,
154194962, 154197827, 154213078, 154215580, 154221423, 154225370,
154227875, 154250998],
'ncbi',
transcript=1,
cds=(154065872, 154250827),
select_transcript=False,
version=3))
db.session.add(TranscriptMapping(
hg19.chromosomes.filter_by(name='chr3').one(),
'refseq',
'NM_000249',
'MLH1',
'forward',
37034841,
37092337,
[37034841, 37038110, 37042446, 37045892, 37048482, 37050305,
37053311, 37053502, 37055923, 37058997, 37061801, 37067128,
37070275, 37081677, 37083759, 37089010, 37090008, 37090395,
37091977],
[37035154, 37038200, 37042544, 37045965, 37048554, 37050396,
37053353, 37053590, 37056035, 37059090, 37061954, 37067498,
37070423, 37081785, 37083822, 37089174, 37090100, 37090508,
37092337],
'ncbi',
transcript=1,
cds=(37035039, 37092144),
select_transcript=False,
version=3))
db.session.commit()
def with_references(*references):
"""
Convenience decorator for parameterizing tests with reference fixtures.
Allows us to write:
@with_references('NM_004006.1', 'NM_004006.2')
def test_references():
pass
Instead of:
@pytest.mark.usefixtures('references')
@pytest.mark.parametrize('references',
[['NM_004006.1', 'NM_004006.2']],
ids=['NM_004006.1,NM_004006.2'],
indirect=True)
def test_references():
pass
"""
def test_with_references(test):
return pytest.mark.usefixtures('references')(
pytest.mark.parametrize('references', [references], indirect=True,
ids=[','.join(references)])(test))
return test_with_references
def with_links(*links):
"""
Convenience decorator for parameterizing tests with transcript-protein
link fixtures.
Allows us to write:
@with_links(('NM_018650', 'NP_061120'), ('NM_027221', None))
def test_links():
pass
Instead of:
@pytest.mark.usefixtures('links')
@pytest.mark.parametrize('links',
[('NM_018650', 'NP_061120'),
('NM_027221', None)],
ids=['NM_018650/NP_061120,NM_027221/*'],
indirect=True)
def test_links():
pass
"""
def test_with_links(test):
return pytest.mark.usefixtures('links')(
pytest.mark.parametrize(
'links', [links], indirect=True,
ids=[','.join('/'.join(a or '*' for a in l)
for l in links)])(test))
return test_with_links