def action(args): if not os.path.exists(args.assembly): raise ValueError("No such file: %s" % (args.assembly,)) for f in args.fastas: if not os.path.exists(f): raise ValueError("No such file: %s" % (f,)) assembly = seqlab.assembly.deserialize(args.assembly) for f in args.fastas: with open(f): for seq in Bio.SeqIO.parse(f, "fasta"): assembly.add_sequence( seq.description, seq.seq.tostring(), align_to=args.align_to if not args.no_alignment else None ) assembly.serialize(args.output if args.output else args.assembly) return 0
def action(args): if not os.path.exists(args.assembly): raise ValueError("No such file: %s" % (args.assembly, )) for f in args.fastas: if not os.path.exists(f): raise ValueError("No such file: %s" % (f, )) assembly = seqlab.assembly.deserialize(args.assembly) for f in args.fastas: with open(f): for seq in Bio.SeqIO.parse(f, 'fasta'): assembly.add_sequence( seq.description, seq.seq.tostring(), align_to=args.align_to if not args.no_alignment else None) assembly.serialize(args.output if args.output else args.assembly) return 0
def action(args): if not os.path.exists(args.first_ab1): raise ValueError("No such file: %s" % (args.first_ab1,)) if not os.path.exists(args.second_ab1): raise ValueError("No such file: %s" % (args.second_ab1,)) if args.metadata and not os.path.exists(args.metadata): raise ValueError("No such file: %s" % (args.metadata)) for f in args.additional_sequences: if not os.path.exists(f): raise ValueError("No such file: %s" % (f,)) assembly = seqlab.contig.ab1toassembly(args.first_ab1, args.second_ab1) if args.metadata: with open(args.metadata) as h: assembly.metadata = json.load(h) for f in args.additional_sequences: with open(f): for seq in Bio.SeqIO.parse(f, 'fasta'): assembly.add_sequence(seq.description, seq.seq.tostring(), align_to='contig') assembly.serialize(args.output) return 0