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from __future__ import absolute_import
from . import test_fasta
from . import test_fastq
import os
import subprocess
import screed
from screed.DBConstants import fileExtension
from . import screed_tst_utils as utils
import shutil
class Test_fa_shell_command(test_fasta.Test_fasta):
"""
Tests the functionality of the 'db' command in creating a
screed database correctly from the shell
"""
def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
cmd = ['screed', 'db', self._testfa]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfa)
def teardown_method(self):
os.unlink(self._testfa + fileExtension)
class Test_fq_shell_command(test_fastq.Test_fastq):
"""
Tests the functionality of the 'db' command in creating a
screed database correctly from the shell
"""
def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfq = utils.get_temp_filename('test.fastq')
shutil.copy(utils.get_test_data('test.fastq'), self._testfq)
cmd = ['screed', 'db', self._testfq]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfq)
def teardown_method(self):
os.unlink(self._testfq + fileExtension)
class Test_fa_shell_module(test_fasta.Test_fasta):
"""
Tests the functionality of the 'db' command in creating a
screed database correctly from the shell
"""
def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
cmd = ['python3', '-m', 'screed', 'db', self._testfa]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfa)
def teardown_method(self):
os.unlink(self._testfa + fileExtension)
class Test_fq_shell_module(test_fastq.Test_fastq):
"""
Tests the functionality of the 'db' command in creating a
screed database correctly from the shell
"""
def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfq = utils.get_temp_filename('test.fastq')
shutil.copy(utils.get_test_data('test.fastq'), self._testfq)
cmd = ['python3', '-m', 'screed', 'db', self._testfq]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfq)
def teardown_method(self):
os.unlink(self._testfq + fileExtension)
class Test_convert_shell(test_fasta.Test_fasta):
"""
Tests the ability to convert a fasta db to a fastq file, parse it into
a fastq db, save to a fasta file, parse the fasta file into a fasta
db and then run the fasta suite, all from the command line.
"""
def setup_method(self):
self._fqName = utils.get_temp_filename('fa_to_fq')
self._faName = utils.get_temp_filename('fq_to_fa')
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
cmd = ['screed', 'db', self._testfa]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
cmd = ['screed', 'dump_fastq', self._testfa, self._fqName]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
cmd = ['screed', 'db', self._fqName]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
cmd = ['screed', 'dump_fasta', self._fqName, self._faName]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
cmd = ['screed', 'db', self._faName]
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._faName)
def teardown_method(self):
os.unlink(self._fqName)
os.unlink(self._fqName + fileExtension)
os.unlink(self._faName)
os.unlink(self._faName + fileExtension)
os.unlink(self._testfa + fileExtension)
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