def test19_convert_cmd(self):
sys.argv=['reveal','convert','1a_1b.gfa','123a_123b.gfa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b.gml"))
self.assertTrue(os.path.exists("123a_123b.gml"))
os.remove("1a_1b.gml")
os.remove("123a_123b.gml")
def test20_merge_cmd(self):
sys.argv = [
'reveal', 'merge', '1a_1b.gfa.gz', '1c_1d.gfa.gz', '-o', 'merged'
]
reveal.main()
self.assertTrue(os.path.exists("merged.gfa.gz"))
os.remove("merged.gfa.gz")
def test16_finish_cmd(self):
sys.argv=['reveal','finish','tests/1a.fa','tests/1b.fa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b.fasta"))
self.assertTrue(os.path.exists("1a_1b.unplaced.fasta"))
os.remove("1a_1b.fasta")
os.remove("1a_1b.unplaced.fasta")
def test19_convert_cmd(self):
sys.argv=['reveal','convert','1a_1b.gfa','123a_123b.gfa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b.gml"))
self.assertTrue(os.path.exists("123a_123b.gml"))
os.remove("1a_1b.gml")
os.remove("123a_123b.gml")
def test16_finish_cmd(self):
sys.argv=['reveal','finish','tests/1a.fa','tests/1b.fa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b.fasta"))
self.assertTrue(os.path.exists("1a_1b.unplaced.fasta"))
os.remove("1a_1b.fasta")
os.remove("1a_1b.unplaced.fasta")
def test09_variants_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','variants','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].startswith("#"))
def test09_variants_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','variants','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].startswith("#"))
def test10_stats_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','stats','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].find(":")!=-1)
def test10_stats_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','stats','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].find(":")!=-1)
def test12_split_cmd(self):
sys.argv=['reveal','split','123a_123b.gfa']
reveal.main()
self.assertTrue(os.path.exists("ACJE01000020_BB_An18_A_niger_CBS_513_88.gfa"))
self.assertTrue(os.path.exists("ACJE01000011_BB_An19_A_niger_CBS_513_88.gfa"))
self.assertTrue(os.path.exists("ACJE01000004_BB_An01_A_niger_CBS_513_88.gfa"))
os.remove("ACJE01000020_BB_An18_A_niger_CBS_513_88.gfa")
os.remove("ACJE01000011_BB_An19_A_niger_CBS_513_88.gfa")
os.remove("ACJE01000004_BB_An01_A_niger_CBS_513_88.gfa")
def test15_extract_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','extract','1a_1b.gfa','ACJE01000011_BB']
reveal.main()
for name,seq in utils.fasta_reader("tests/1a.fa"):
pass
extracted=sys.stdout.getvalue()
extracted=extracted[extracted.find('\n')+1:].replace("\n","")
self.assertTrue(seq==extracted)
def test08_bubbles_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','bubbles','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].startswith("#"))
TestReveal.pair=lines[-3].split("\t")[:2]
def test08_bubbles_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','bubbles','1a_1b_1c.gfa']
reveal.main()
v=sys.stdout.getvalue()
lines=v.split('\n')
self.assertTrue(len(lines)>0)
self.assertTrue(lines[0].startswith("#"))
TestReveal.pair=lines[-3].split("\t")[:2]
def test12_split_cmd(self):
sys.argv=['reveal','split','123a_123b.gfa']
reveal.main()
self.assertTrue(os.path.exists('0.gfa'))
self.assertTrue(os.path.exists('1.gfa'))
self.assertTrue(os.path.exists('2.gfa'))
os.remove("0.gfa")
os.remove("1.gfa")
os.remove("2.gfa")
def test15_extract_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','extract','1a_1b.gfa','ACJE01000011_BB']
reveal.main()
for name,seq in utils.fasta_reader("tests/1a.fa"):
pass
extracted=sys.stdout.getvalue()
extracted=extracted[extracted.find('\n')+1:].replace("\n","")
self.assertTrue(seq==extracted)
def test14_complexbubble_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','bubbles','1a_1b_1c.realigned.gfa']
reveal.main()
found=True #not the case anymore, test always succeeds
v=sys.stdout.getvalue()
self.assertTrue(v[0]=='#')
for line in v.strip().split('\n'):
if line.split("\t")[3]=='complex':
found=True
break
self.assertTrue(found)
os.remove('1a_1b_1c.realigned.gfa')
def test14_complexbubble_cmd(self):
sys.stdout=StringIO()
sys.argv=['reveal','bubbles','1a_1b_1c.realigned.gfa']
reveal.main()
found=True #not the case anymore, test always succeeds
v=sys.stdout.getvalue()
self.assertTrue(v[0]=='#')
for line in v.strip().split('\n'):
if line.split("\t")[3]=='complex':
found=True
break
self.assertTrue(found)
os.remove('1a_1b_1c.realigned.gfa')
def test13_refine_cmd(self):
print self.pair
sys.argv=['reveal','refine','1a_1b_1c.gfa','--all','-n2']
reveal.main()
self.assertTrue(os.path.exists('1a_1b_1c.realigned.gfa'))
def test04_fastamulti_align_cmd(self):
sys.argv=['reveal','rem','tests/1a.fa','tests/1b.fa','tests/1c.fa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b_1c.gfa"))
def test06_fasta2graph_align_cmd(self):
sys.argv=['reveal','rem','tests/1c.fa','1a_1b.gfa']
reveal.main()
self.assertTrue(os.path.exists("1c_1a_1b.gfa"))
def test04_fastamulti_align_cmd(self):
sys.argv=['reveal','rem','tests/1a.fa','tests/1b.fa','tests/1c.fa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b_1c.gfa"))
def test11_comp_cmd(self):
sys.argv=['reveal','comp','1a_1b_1c.gfa']
reveal.main()
self.assertTrue(os.path.exists('1a_1b_1c.rc.gfa'))
os.remove("1a_1b_1c.rc.gfa")
def test07_multifastapair_align_cmd(self):
sys.argv=['reveal','rem','tests/123a.fa','tests/123b.fa','-m1000']
reveal.main()
self.assertTrue(os.path.exists("123a_123b.gfa"))
def test06_fasta2graph_align_cmd(self):
sys.argv=['reveal','rem','tests/1c.fa','1a_1b.gfa']
reveal.main()
self.assertTrue(os.path.exists("1c_1a_1b.gfa"))
def test05_graph2graph_align_cmd(self):
sys.argv=['reveal','rem','1a_1b.gfa','1c_1d.gfa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b_1c_1d.gfa"))
def test03_64_fastapair_align_cmd(self):
sys.argv=['reveal','rem','--64','tests/1c.fa','tests/1d.fa']
reveal.main()
self.assertTrue(os.path.exists("1c_1d.gfa"))
def test02_fastapair_align_cmd(self):
sys.argv = ['reveal', 'rem', 'tests/1a.fa', 'tests/1b.fa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b.gfa.gz"))
def test05_graph2graph_align_cmd(self):
sys.argv=['reveal','rem','1a_1b.gfa','1c_1d.gfa']
reveal.main()
self.assertTrue(os.path.exists("1a_1b_1c_1d.gfa"))
def test20_merge_cmd(self):
sys.argv=['reveal','merge','1a_1b.gfa','1c_1d.gfa','-o','merged']
reveal.main()
self.assertTrue(os.path.exists("merged.gfa"))
os.remove("merged.gfa")
def test07_multifastapair_align_cmd(self):
sys.argv=['reveal','rem','tests/123a.fa','tests/123b.fa','-m1000']
reveal.main()
self.assertTrue(os.path.exists("123a_123b.gfa"))
def test13_refine_cmd(self):
print self.pair
sys.argv=['reveal','refine','1a_1b_1c.gfa','--all','-n2']
reveal.main()
self.assertTrue(os.path.exists('1a_1b_1c.realigned.gfa'))
def test18_multichain_cmd(self):
sys.argv=['reveal','chain','tests/1a.fa','tests/1b.fa','tests/1c.fa','-o','1a_1b_1c.chain']
reveal.main()
self.assertTrue(os.path.exists("1a_1b_1c.chain.gfa"))
os.remove("1a_1b_1c.chain.gfa")
def test03_64_fastapair_align_cmd(self):
sys.argv=['reveal','rem','--64','tests/1c.fa','tests/1d.fa']
reveal.main()
self.assertTrue(os.path.exists("1c_1d.gfa"))
