def setUp(self):
self.a = glbase3.delayedlist(
filename="test_data/array_data.csv",
format=format) # although I don't actually need this at all.
spoof_gl = [{"name": "Lypla1"}, {"name": "Pdia4"}]
self.b = glbase3.genelist()
self.b.load_list(spoof_gl)
def test_sam_tophat_xs(self):
newgl = gl.genelist("test_data/test.sam",
format=gl.format.sam_tophat_xs)
self.assertEqual(newgl[0]["loc"], "chr1:3035081-3035081")
self.assertEqual(
newgl[0]["seq"],
"AAACATTCCTGGGAACATCTTGACCATAAGATAAAGGGGACTGTGAAGACATAGCAGGGCTATATTATCTAAGTCAACACCATCTGGCCG"
)
self.assertEqual(newgl[0]["strand"], "+")
self.assertEqual(newgl[1]["strand"], "-")
# test it also works for a delayedlist, which is where I'd usually use it:
newgl = gl.delayedlist("test_data/test.sam",
format=gl.format.sam_tophat_xs)
for index, item in enumerate(newgl):
#print item
if index == 0:
self.assertEqual(item["loc"], "chr1:3035081-3035081")
self.assertEqual(
item["seq"],
"AAACATTCCTGGGAACATCTTGACCATAAGATAAAGGGGACTGTGAAGACATAGCAGGGCTATATTATCTAAGTCAACACCATCTGGCCG"
)
self.assertEqual(item["strand"], "+")
elif index == 1:
self.assertEqual(item["strand"], "-")
def test_gzipped_delayedlist(self):
self.b = glbase3.genelist(filename="test_data/array_data.csv",
format=format)
self.a = glbase3.delayedlist(filename="test_data/array_data.csv.gz",
format=format,
gzip=True)
self.assertEqual(len(self.a), len(self.b))
for item in self.a:
self.assertEqual(item["name"], "Lypla1")
self.assertEqual(item["array_systematic_name"], 'scl000965.1_10-S')
break
def test_force_tsvarg(self):
form = dict(tss_loc=1, skiplines=0) # This loads tss_loc as strings
form_delayed = dict(tss_loc=1, skiplines=0) # delayedlists must have skiplines
a = gl.genelist(filename="test_data/mm9_refGene.tsv", force_tsv=True, format=form)
c = gl.delayedlist(filename="test_data/mm9_refGene.tsv", format=form, force_tsv=True)
d = gl.genome(filename="test_data/mm9_refGene.tsv", format=form_delayed, force_tsv=True)
e = gl.expression(filename="test_data/mm9_refGene.tsv", format=form, force_tsv=True, expn="column[5:]") # fake array data # must go last as it modifies format
# Make sure glbase is not just bodging it all in in one key:
self.assertEqual("chr1:134212701-134212701", a[0]["tss_loc"])
self.assertEqual("chr1:134212701-134212701", c[0]["tss_loc"])
self.assertEqual("chr1:134212701-134212701", d[0]["tss_loc"]) # dls should work as __getitem__() will return the zeroth entry.
self.assertEqual("chr1:134212701-134212701", e[0]["tss_loc"])
def test_force_tsv_format(self):
form = dict(tss_loc=1, force_tsv=True, chr=1)
form_delayed = dict(tss_loc=1, force_tsv=True, skiplines=0) # delayedlists must have skiplines
a = gl.genelist(filename="test_data/mm9_refGene.tsv", format=form)
c = gl.delayedlist(filename="test_data/mm9_refGene.tsv", format=form_delayed)
d = gl.genome(filename="test_data/mm9_refGene.tsv", format=form)
e = gl.expression(filename="test_data/mm9_refGene.tsv", format=form, expn="column[5:]") # must go last as it modifies format
# Make sure glbase is not just bodging it all in in one key:
self.assertEqual("chr1:134212701-134212701", a[0]["tss_loc"])
self.assertEqual("chr1:134212701-134212701", c[0]["tss_loc"])
self.assertEqual("chr1:134212701-134212701", d[0]["tss_loc"])
self.assertEqual("chr1:134212701-134212701", e[0]["tss_loc"])
def test_len(self):
self.b = glbase3.genelist(filename="test_data/array_data.csv",
format=format)
self.a = glbase3.delayedlist(filename="test_data/array_data.csv",
format=format)
self.assertEqual(len(self.a), len(self.b))