def test_outputbasename(self):
''' Test that the outputfile parameter works with just a basename '''
os.mkdir('basename')
os.symlink(self.sff, os.path.join('basename', 'sff1.sff'))
outfile = bwa.compile_reads('basename', 'outputfile.fastq')
eq_('outputfile.fastq', outfile)
eq_(seqio.reads_in_file(self.sff), seqio.reads_in_file(outfile))
def test_outputabsrelpath(self):
''' Test that the outputfile parameter works with a relative or abs path '''
os.mkdir('absrel')
os.symlink(self.sff, os.path.join('absrel', 'sff1.sff'))
outfile = bwa.compile_reads('absrel', 'absrel/outputfile.fastq')
eq_('absrel/outputfile.fastq', outfile)
eq_(seqio.reads_in_file(self.sff),
seqio.reads_in_file('absrel/outputfile.fastq'))
def test_paramdirfastqonly(self):
''' Directory of only fastq '''
os.mkdir('fastq')
os.symlink(self.fastq, os.path.join('fastq', 'fq1.fastq'))
os.symlink(self.fastq, os.path.join('fastq', 'fq2.fastq'))
outfile = bwa.compile_reads('fastq')
expected_readcount = seqio.reads_in_file(self.sff) * 2
self._isfastq(outfile)
eq_(expected_readcount, seqio.reads_in_file(outfile))
def test_paramdirsffonly(self):
''' Directory of only sff files '''
os.mkdir('sffs')
os.symlink(self.sff, os.path.join('sffs', 'sff1.sff'))
os.symlink(self.sff, os.path.join('sffs', 'sff2.sff'))
outfile = bwa.compile_reads('sffs')
expected_readcount = seqio.reads_in_file(self.sff) * 2
self._isfastq(outfile)
eq_(expected_readcount, seqio.reads_in_file(outfile))
def test_targetbug1_3(self):
'''
Targets a bug where compile_reads would generate 2 identical
fastq files(reads.fastq and sff.fastq)
'''
os.mkdir('sffs3')
sffpth = os.path.join('sffs3', 'sff1.sff')
os.symlink(self.sff, sffpth)
outfile = bwa.compile_reads(sffpth)
fastqs = glob.glob('*.fastq')
assert len(fastqs) == 1, fastqs
def test_paramdirmixed(self):
''' Directory of sff & fastq '''
os.mkdir('mixed')
os.symlink(self.sff, os.path.join('mixed', 'sff1.sff'))
os.symlink(self.fastq, os.path.join('mixed', 'fq1.fastq'))
outfile = bwa.compile_reads('mixed')
expected_readcount = seqio.reads_in_file( self.sff ) + \
seqio.reads_in_file( self.fastq )
self._isfastq(outfile)
eq_(expected_readcount, seqio.reads_in_file(outfile))
def test_paramsinglefastq(self):
''' Input fastq should not be changed '''
stat = os.stat(self.fastq)
outfile = bwa.compile_reads(self.fastq)
eq_(stat.st_mtime, os.stat(self.fastq).st_mtime)
eq_(stat.st_ino, os.stat(outfile).st_ino)
def test_paramsinglesff(self):
''' Make sure single sff works '''
outfile = bwa.compile_reads(self.sff)
self._isfastq(outfile)
def test_noreads(self):
''' Directory empty '''
os.mkdir('emptydir')
outfile = bwa.compile_reads('emptydir')
eq_([], outfile)
