def test_direxistnofiles( self ):
''' No fastq or sff in dir_path but has other files '''
os.mkdir( 'somedir' )
open( 'somedir/somefile.fasta', 'w' ).close()
open( 'somedir/somefile.fast', 'w' ).close()
open( 'somedir/somefile.s', 'w' ).close()
open( 'somedir/somefile.sffo', 'w' ).close()
eq_( [], seqio.get_reads( 'somedir' ) )
def test_direxistnofiles(self):
''' No fastq or sff in dir_path but has other files '''
os.mkdir('somedir')
open('somedir/somefile.fasta', 'w').close()
open('somedir/somefile.fast', 'w').close()
open('somedir/somefile.s', 'w').close()
open('somedir/somefile.sffo', 'w').close()
eq_([], seqio.get_reads('somedir'))
def test_returnlist( self ):
''' Should return list of sff and fastq files with dir_path prefix '''
os.mkdir( 'hasreads' )
reads = [
'hasreads/file1.fastq',
'hasreads/file2.fastq',
'hasreads/file3.sff',
'hasreads/file4.sff',
]
for read in reads:
open( read, 'w' ).close()
eq_( sorted(reads), sorted(seqio.get_reads( 'hasreads' )) )
def test_returnlist(self):
''' Should return list of sff and fastq files with dir_path prefix '''
os.mkdir('hasreads')
reads = [
'hasreads/file1.fastq',
'hasreads/file2.fastq',
'hasreads/file3.sff',
'hasreads/file4.sff',
]
for read in reads:
open(read, 'w').close()
eq_(sorted(reads), sorted(seqio.get_reads('hasreads')))
def test_emptydir( self ):
''' Empty directory '''
os.mkdir( 'somedir2' )
eq_( [], seqio.get_reads( 'somedir2' ) )
def test_dirpath_notdir( self ):
''' dir_path is not a directory '''
open( 'somefile', 'w' ).close()
seqio.get_reads( 'somefile' )
def test_invaliddirpath( self ):
''' dir_path param is non existant '''
seqio.get_reads( '/not/exist' )
def test_emptydir(self):
''' Empty directory '''
os.mkdir('somedir2')
eq_([], seqio.get_reads('somedir2'))
def test_dirpath_notdir(self):
''' dir_path is not a directory '''
open('somefile', 'w').close()
seqio.get_reads('somefile')
def test_invaliddirpath(self):
''' dir_path param is non existant '''
seqio.get_reads('/not/exist')
