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', '-'))])