def test_save_fasta(self):
genome_mm10 = glbase3.genome()
genome_mm10.bindSequence("test_data/seq")
newl = [{
"name": "A",
"loc": glbase3.location(loc="chr1:100-150")
}, {
"name": "X",
"loc": glbase3.location(loc="chrA:100-150")
}]
newgl = glbase3.genelist()
newgl.load_list(newl)
fasta = genome_mm10.getSequences(newgl)
fasta.saveFASTA(filename="/tmp/test_fasta.fa", name=["loc", "name"])
with open("/tmp/test_fasta.fa") as oh:
self.assertEqual(oh.readline().strip(), '>chr1:100-150_A')
self.assertEqual(
oh.readline().strip(),
'ATCAGACAGGTAGATCATCTCGCTCCGAGCTTGCCACCAGCAAACCATTGC')
self.assertEqual(oh.readline().strip(), '>chrA:100-150_X')
self.assertEqual(
oh.readline().strip(),
'GTAAAAACCCGATGGAATACTCATCCAGTAAGTCCGAACCACTTCAACATC')
fasta.saveFASTA(filename="/tmp/test_fasta.fa")
with open("/tmp/test_fasta.fa") as oh:
self.assertEqual(oh.readline().strip(), '>chr1:100-150')
self.assertEqual(
oh.readline().strip(),
'ATCAGACAGGTAGATCATCTCGCTCCGAGCTTGCCACCAGCAAACCATTGC')
self.assertEqual(oh.readline().strip(), '>chrA:100-150')
self.assertEqual(
oh.readline().strip(),
'GTAAAAACCCGATGGAATACTCATCCAGTAAGTCCGAACCACTTCAACATC')
def test_get_sequences(self):
genome_mm10 = glbase3.genome()
genome_mm10.bindSequence("test_data/seq")
seq = genome_mm10.getSequence("chr1:100-150")
self.assertEqual(
seq, 'ATCAGACAGGTAGATCATCTCGCTCCGAGCTTGCCACCAGCAAACCATTGC')
seq = genome_mm10.getSequence("chrA:100-150")
self.assertEqual(
seq, 'GTAAAAACCCGATGGAATACTCATCCAGTAAGTCCGAACCACTTCAACATC')
def test_tsv_sniffer_force(self):
# These are all tsv files
# sniffer correctly loads locations.
a = gl.genelist(filename="test_data/mm9_refGene.tsv", force_tsv=True, format=gl.format.sniffer)
d = gl.genome(filename="test_data/mm9_refGene.tsv", force_tsv=True, format=gl.format.sniffer)
# Microarrays and delayedlists can't be sniffed
# 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", d[0]["tss_loc"])
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 setUp(self):
self.a = glbase3.genelist(filename="test_data/testA.csv",
format=glbase3.format.sniffer)
self.g = glbase3.genome(filename="test_data/test-genome.csv",
format=glbase3.format.sniffer)