def test_fa_to_bed(self):
# test with and without offsets
# start with block of FASTA formatted sequence:
# two blocks on same chromosome
# additional block on next chromosome
# additional block on next chromosome
# two blocks on chrA, one on chrB
# test without offset
self.maxDiff = None
reader = cStringIO.StringIO(CROSSMAP_BLOCK)
# test without offset
blocks1 = list(fa_to_bed(reader, 25, offset=0))
self.assertListEqual(blocks1, CROSSMAP1)
# test with offset
reader = cStringIO.StringIO(CROSSMAP_BLOCK)
blocks2 = list(fa_to_bed(reader, 25, offset=1000))
self.assertListEqual(blocks2, CROSSMAP2)
def test_fa_to_bed(self):
# test with and without offsets
# start with block of FASTA formatted sequence:
# two blocks on same chromosome
# additional block on next chromosome
# additional block on next chromosome
# two blocks on chrA, one on chrB
# test without offset
self.maxDiff = None
reader = cStringIO.StringIO(CROSSMAP_BLOCK)
# test without offset
blocks1 = list(fa_to_bed(reader,25,offset=0))
self.assertListEqual(blocks1,CROSSMAP1)
# test with offset
reader = cStringIO.StringIO(CROSSMAP_BLOCK)
blocks2 = list(fa_to_bed(reader,25,offset=1000))
self.assertListEqual(blocks2,CROSSMAP2)
def test_fa_to_bed_throws_expected_error(self):
# test with and without offsets
# start with unsorted FASTA block
# grab chrA only and randomize order
reads = cStringIO.StringIO(SHORT_FASTA_KMERS).read().split("\n")
reads = reads[40:50] + reads[30:40] + reads[0:16] + reads[20:30]
reads = "\n".join(reads)
reader = cStringIO.StringIO(reads)
# fa_to_bed is a generator, so we need to create a callable to make
# it a list for it to actually raise the error
tfunc = lambda x, y, z: list(fa_to_bed(x, y, offset=z))
self.assertRaises(MalformedFileError, tfunc, reader, 25, 0)
reader = cStringIO.StringIO(reads)
self.assertRaises(MalformedFileError, tfunc, reader, 25, 1000)
reader = cStringIO.StringIO(reads)
self.assertRaises(MalformedFileError, tfunc, reader, 15, 0)
def test_fa_to_bed_throws_expected_error(self):
# test with and without offsets
# start with unsorted FASTA block
# grab chrA only and randomize order
reads = cStringIO.StringIO(SHORT_FASTA_KMERS).read().split("\n")
reads = reads[40:50] + reads[30:40] + reads[0:16] + reads[20:30]
reads = "\n".join(reads)
reader = cStringIO.StringIO(reads)
# fa_to_bed is a generator, so we need to create a callable to make
# it a list for it to actually raise the error
tfunc = lambda x,y,z: list(fa_to_bed(x,y,offset=z))
self.assertRaises(MalformedFileError,tfunc,reader,25,0)
reader = cStringIO.StringIO(reads)
self.assertRaises(MalformedFileError,tfunc,reader,25,1000)
reader = cStringIO.StringIO(reads)
self.assertRaises(MalformedFileError,tfunc,reader,15,0)
