def test_load():
engine = create_engine('sqlite://')
metadata = waldo.goslim.models.Base.metadata
metadata.bind = engine
metadata.create_all()
sessionmaker_ = sessionmaker(engine)
nr_entries, nr_aspects = waldo.goslim.load.load(testdir, sessionmaker_)
inputfile = open(path_to_testfile(waldo.goslim.load._inputfilename))
nr_lines = len(inputfile.readlines())
assert nr_entries == (nr_lines-1)
aspects = set()
inputfile = open(path_to_testfile(waldo.goslim.load._inputfilename))
lines = inputfile.readlines()
for line in lines[1:]:
tokens = line.strip().split('\t')
aspects.add(tokens[-2])
assert len(aspects) == nr_aspects
session = sessionmaker_()
name = waldo.goslim.goslim.map_to_goslim('GO:0014709', 'mgi', session)
assert name == 'developmental processes'
nonexistent = waldo.goslim.goslim.map_to_goslim('GO:99999', 'mgi', session)
assert nonexistent is None
from sqlalchemy.orm import sessionmaker
import re
import gzip
import waldo.backend
import waldo.uniprot.load
import waldo.uniprot.models
import waldo.uniprot.retrieve
import waldo.go.load
import waldo.go.go
from waldo.translations.models import Translation
from .backend import testdir as _testdir
from waldo.tests.backend import path_to_testfile
_testfile = path_to_testfile('uniprot_sprot.xml.gz')
_mapping_testfile = path_to_testfile('idmapping_selected.tab.gz')
def load_uniprot_test():
from waldo.tests.test_go import load_go
engine = create_engine('sqlite://')
metadata = waldo.uniprot.models.Base.metadata
metadata.bind = engine
metadata.create_all()
conn = engine.connect()
if waldo.backend.use_fts:
conn.execute("drop table uniprot_entry")
conn.execute("CREATE VIRTUAL TABLE uniprot_entry USING fts4 (" +
"name VARCHAR(32) NOT NULL, " +
"rname VARCHAR(128) NOT NULL, " +
def test_read():
seqs = list(fasta.read(path_to_testfile('test.fasta')))
assert len(seqs) == 2
assert seqs[1].header.find('gene:ENSMUSG00000064345')
assert seqs[1].header[-1] != '\n'
assert seqs[1].header[0] != '>'