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from __future__ import absolute_import
from . import test_fasta
import os
import screed
from screed.DBConstants import fileExtension
from . import screed_tst_utils as utils
import shutil
class Test_fasta_to_fastq(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
"""
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)
screed.read_fasta_sequences(self._testfa)
screed.ToFastq(self._testfa, self._fqName) # Fasta db -> fasta text
screed.read_fastq_sequences(self._fqName) # Fastq file -> fastq db
screed.ToFasta(self._fqName, self._faName) # Fastq db -> fasta text
screed.read_fasta_sequences(self._faName) # Fasta file -> fasta db
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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