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