parser.add_argument("--keep-temporary-files",
action='store_true',
help="don't clean up")
parser.add_argument("--chunk-size",
default=10,
type=int,
help="don't clean up")
parser.add_argument("--nthreads",
default=1,
type=int,
help="Number of threads to use in alignment")
args = parser.parse_args()
#refname = f"config/reference.gb"
refname = args.gbk
features = load_features(refname)
seqs = SeqIO.parse(args.sequences, 'fasta')
ref = SeqIO.read(refname, 'genbank')
#clade_designations = read_in_clade_definitions(f"config/clades.tsv")
clade_designations = read_in_clade_definitions(args.clade)
log_fname = "clade_assignment.log"
in_fname = "clade_assignment_tmp.fasta"
out_fname = "clade_assignment_tmp_alignment.fasta"
output = open(args.output, 'w')
print('name\tclade\tparent clades', file=output)
# break the sequences into chunks, align each to the reference, and assign clades one-by-one
done = False
while not done:
parser = argparse.ArgumentParser(
description="Add translations",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('--tree', type=str, required=True, help="input tree")
parser.add_argument('--reference', type=str, required=True, help="reference genbank sequence")
parser.add_argument('--translations', type=str, nargs='+', required=True, help="amino acid alignment")
parser.add_argument('--genes', type=str, nargs='+', required=True, help="amino acid alignment")
parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON")
args = parser.parse_args()
genes = args.genes if type(args.genes)==list else [args.genes]
translations = args.translations if type(args.translations)==list else [args.translations]
ref = SeqIO.read(args.reference, format='genbank')
features = load_features(args.reference)
if not set(features.keys())==set(args.genes):
print("WARNING: supplied genes don't match the annotation")
print("the following features are in the annotation by not supplied as genes:", set(features.keys()).difference(args.genes))
print("the following features are in the supplied as genes but not the annotation:", set(args.genes).difference(features.keys()))
T = Phylo.read(args.tree, 'newick')
leafs = {n.name for n in T.get_terminals()}
node_data = {}
root_sequence_translations = {}
for gene, translation in zip(genes, translations):
seqs = []
for s in SeqIO.parse(translation, 'fasta'):
if s.id in leafs:
sequences = []
for seq in SeqIO.parse(args.sequences, 'fasta'):
if seq.name in metadata:
if metadata[seq.name]["num_date"]>=time_interval[0] and \
metadata[seq.name]["num_date"]<time_interval[1] and \
metadata[seq.name]["region"]==region:
sequences.append(seq)
tmp_str = "".join(sample('ABCDEFGHILKLMOPQRSTUVWXYZ', 20))
if not os.path.isdir('tmp'):
os.mkdir('tmp')
print("selected %d for region %s and date interval %f-%f" %
(len(sequences), region, time_interval[0], time_interval[1]))
features_to_translate = load_features(args.reference_sequence, args.genes)
tmp_file = "tmp/sequence_file_%s_%s.fasta" % (region, tmp_str)
tmp_file_out = "tmp/sequence_file_%s_%s_aln.fasta" % (region, tmp_str)
SeqIO.write(sequences, tmp_file, 'fasta')
fail = align.run(
pseudo_args(sequences=tmp_file,
reference_sequence=args.reference_sequence,
output=tmp_file_out,
reference_name=None,
remove_reference=True,
method='mafft',
nthreads=1,
fill_gaps=False))
if fail:
sys.exit(fail)
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Translate nucleotide sequences to amino acid sequences for the requested genes",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('--sequences', required=True, help='FASTA file of nucleotide sequences to translate')
parser.add_argument('--reference-sequence', required=True, help='GenBank or GFF file containing the annotation')
parser.add_argument('--genes', nargs='+', help="genes to translate (list or file containing list)")
parser.add_argument('--output', nargs='+', help="FASTA files of amino acid sequences per gene")
args = parser.parse_args()
# Load features for requested genes.
features = load_features(args.reference_sequence, args.genes)
# Load sequences indexed by sequence id.
sequences = {
sequence.id: str(sequence.seq)
for sequence in Bio.SeqIO.parse(args.sequences, "fasta")
if "N" not in str(sequence.seq)
}
#if sorted(set(list(str(sequence.seq)))) == ["A", "C", "G", "T"]
# Translate requested genes.
translations = {}
invalid_samples = set()
for feature_name, output_file in zip(args.genes, args.output):
translations[feature_name] = translate_feature(sequences, features[feature_name])
records = [