def action(args):
if not os.path.exists(args.assembly):
raise ValueError("No such file: %s" % (args.assembly, ))
asm = deserialize(args.assembly)
s = "<!DOCTYPE html><html><body>" + renderassembly(asm) + "</body></html>"
if args.output:
with open(args.output, 'w') as out:
print >> out, s
else:
print s
return 0
def action(args):
if not os.path.exists(args.assembly):
raise ValueError("No such file: %s" % (args.assembly,))
asm = deserialize(args.assembly)
s = "<!DOCTYPE html><html><body>" + renderassembly(asm) + "</body></html>"
if args.output:
with open(args.output, 'w') as out:
print >>out, s
else:
print s
return 0
def test_addsequences(tmpdir):
a = asm.Assembly([('a', asm.aflist(0, 'ATGATGGA', '-'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
with open(str(tmpdir.join('a.fasta')), 'w') as h:
print >>h, '>alpha omega\nTGATGGA\n'
class Args:
assembly=str(tmpdir.join('asm.json.bz2'))
output=str(tmpdir.join('output.json.bz2'))
align_to='a'
fastas=[str(tmpdir.join('a.fasta'))]
no_alignment=False
assert seqlab.subcommands.addsequence.action(Args()) == 0
assert os.path.exists(str(tmpdir.join('output.json.bz2')))
asm2 = asm.deserialize(str(tmpdir.join('output.json.bz2')))
assert asm2 == asm.Assembly([('a', asm.aflist(0, 'ATGATGGA', '-')),
('alpha omega', asm.aflist(1, 'TGATGGA', '-'))])
