def main():
parser = argparse.ArgumentParser(
description="concat_fasta",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--input_dir',
type=dir_path,
required=True,
help="dir with fasta")
parser.add_argument('--extra_fasta_files', nargs='+', default=[], help="extra fasta file list to include in the " \
"sequence")
parser.add_argument('--output',
type=str,
required=True,
help="output fasta")
args = parser.parse_args()
in_dir = args.input_dir
out_file = args.output
in_extra = args.extra_fasta_files
in_fasta = glob.glob("{}/*fasta".format(in_dir))
sequences = read_sequences(*in_fasta, *in_extra)
Bio.SeqIO.write(sequences, out_file, 'fasta')
import argparse
from augur.align import read_sequences
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="Combine and dedup FASTAs",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--input',
type=str,
nargs="+",
metavar="FASTA",
required=True,
help="input FASTAs")
parser.add_argument('--output',
type=str,
metavar="FASTA",
required=True,
help="output FASTA")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = read_sequences(*args.input)
# Convert dictionary of sequences by id to a list, for compatibility with
# augur versions <9.0.0.
if isinstance(sequences, dict):
sequences = list(sequences.values())
SeqIO.write(sequences, args.output, 'fasta')
def test_read_seq_compare(self):
data_file = pathlib.Path("tests/data/align/aa-seq_h3n2_ha_2y_2HA1_dup.fasta")
with pytest.raises(align.AlignmentError):
assert align.read_sequences(str(data_file))
def test_read_sequences(self):
data_file = pathlib.Path('tests/data/align/test_aligned_sequences.fasta')
result = align.read_sequences(str(data_file))
assert len(result) == 4
import argparse
from augur.align import read_sequences
from Bio import SeqIO
from pathlib import Path
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--sequences", required=True, nargs="+", help="FASTA file of sequences to partition into smaller chunks")
parser.add_argument("--sequences-per-group", required=True, type=int, help="number of sequences to include in each group")
parser.add_argument("--output-dir", required=True, help="directory to write out partitioned sequences")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = list(read_sequences(*args.sequences).values())
# Create the requested output directory.
output_dir = Path(args.output_dir)
output_dir.mkdir(exist_ok=True)
# Determine partition indices.
indices = list(range(0, len(sequences), args.sequences_per_group))
# Add a final index to represent the end of the last partition.
if indices[-1] != len(sequences):
indices.append(len(sequences))
# Partition sequences into groups of no more than the requested number.
for i in range(len(indices) - 1):
# Save partitioned sequences to a new FASTA file named after the partition number.
"--sequences",
required=True,
nargs="+",
help="FASTA file of sequences to partition into smaller chunks")
parser.add_argument("--sequences-per-group",
required=True,
type=int,
help="number of sequences to include in each group")
parser.add_argument("--output-dir",
required=True,
help="directory to write out partitioned sequences")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = read_sequences(*args.sequences)
# Convert dictionary of sequences by id to a list, for compatibility with
# augur versions <9.0.0.
if isinstance(sequences, dict):
sequences = list(sequences.values())
# Create the requested output directory.
output_dir = Path(args.output_dir)
output_dir.mkdir(exist_ok=True)
# Determine partition indices.
indices = list(range(0, len(sequences), args.sequences_per_group))
# Add a final index to represent the end of the last partition.
if indices[-1] != len(sequences):
from Bio import SeqIO
import argparse
from augur.align import read_sequences
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="Combine and dedup FASTAs",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--input',
type=str,
nargs="+",
metavar="FASTA",
required=True,
help="input FASTAs")
parser.add_argument('--output',
type=str,
metavar="FASTA",
required=True,
help="output FASTA")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = list(read_sequences(*args.input).values())
SeqIO.write(sequences, args.output, 'fasta')
from Bio import SeqIO
import argparse
from augur.align import read_sequences
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="Combine and dedup FASTAs",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('--input', type=str, nargs="+", metavar="FASTA", required=True, help="input FASTAs")
parser.add_argument('--output', type=str, metavar="FASTA", required=True, help="output FASTA")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = list(read_sequences(*args.input))
SeqIO.write(sequences, args.output, 'fasta')
"--sequences",
required=True,
nargs="+",
help="FASTA file of sequences to partition into smaller chunks")
parser.add_argument("--sequences-per-group",
required=True,
type=int,
help="number of sequences to include in each group")
parser.add_argument("--output-dir",
required=True,
help="directory to write out partitioned sequences")
args = parser.parse_args()
# Read sequences with augur to benefit from additional checks for duplicates.
sequences = list(read_sequences(*args.sequences))
# Create the requested output directory.
output_dir = Path(args.output_dir)
output_dir.mkdir(exist_ok=True)
# Determine partition indices.
indices = list(range(0, len(sequences), args.sequences_per_group))
# Add a final index to represent the end of the last partition.
if indices[-1] != len(sequences):
indices.append(len(sequences))
# Partition sequences into groups of no more than the requested number.
for i in range(len(indices) - 1):
# Save partitioned sequences to a new FASTA file named after the partition number.