def extract_seq_ids(data, fmt='fasta', variant=None):
"""
Given FASTQ-format data (string), parse out only the
sequence IDs and return.
"""
fh = StringIO(data)
if fmt == 'fastq':
sc = SequenceCollection.read(fh, format=fmt, variant=variant)
else:
sc = SequenceCollection.read(fh, format=fmt)
return frozenset(entry.id for entry in sc)
def extract_seq_ids(data, fmt='fasta', variant=None):
"""
Given FASTQ-format data (string), parse out only the
sequence IDs and return.
"""
fh = StringIO(data)
if fmt == 'fastq':
sc = SequenceCollection.read(fh, format=fmt, variant=variant)
else:
sc = SequenceCollection.read(fh, format=fmt)
return frozenset(entry.id for entry in sc)
def convert_phylip(infile, outfile, format):
seqs = SequenceCollection.read(
infile, format='phylip',
data_parser=phylip.relaxed_ids
)
seqs.write(outfile, format=format)
def main():
args = handle_program_options()
if osp.isfile(args.out_dir):
print("--out_dir (-o) option must be a valid directory and not a file",
file=sys.stderr)
sys.exit(1)
# will fail gracefully if dir exists
skbu.create_dir(args.out_dir)
metagenomes = []
if args.metagenome_id is not None:
metagenomes.append(args.metagenome_id)
elif args.metagenome_file is not None:
metagenomes.extend(parse_metagenome_file(args.metagenome_file))
if args.verbose:
msg = 'Processing requested for {} metagenome(s) found in: {}'
print(msg.format(len(metagenomes), args.metagenome_file))
# MG-RAST stage.file ids for downloading
derep_passed = '150.1'
screen_passed = '299.1'
for mg_id in metagenomes:
if args.verbose:
print('Processing metagenome: {}'.format(mg_id))
print('\tDownloading: Dereplication Passed...', end='')
sys.stdout.flush()
derepp_rsp = mgapi.mgrast_request('download', mg_id,
{'file': derep_passed},
auth_key=args.auth_key)
derepp_sc = SequenceCollection.read(StringIO(derepp_rsp.text),
format='fastq',
variant='illumina1.8')
if args.verbose:
print('{} sequences'.format(len(derepp_sc)))
print('\tDownloading: Screen Passed...', end='')
sys.stdout.flush()
screenp_rsp = mgapi.mgrast_request('download', mg_id,
{'file': screen_passed},
auth_key=args.auth_key)
screenp_ids = extract_seq_ids(screenp_rsp.text, fmt='fastq',
variant='illumina1.8')
if args.verbose:
print('{} sequences'.format(len(screenp_ids)))
# filter dereplication passed with IDs from screen passed
failed_screen = filter_seqs(derepp_sc, screenp_ids)
if args.verbose:
nsp = len(screenp_ids)
print('\tRemoved {} sequences from Dereplication Passed'.format(nsp))
print('\tleaving {} sequences'.format(len(failed_screen)))
out_fp = osp.join(args.out_dir, mg_id + '_screen_failed.fastq')
failed_screen.write(out_fp, format='fastq', variant='illumina1.8')
if args.verbose:
print('Sequence data written to: ' + out_fp)
def test_make_mini_otu_files(self):
os.system("mkdir tmp")
self.extension_seqs = SequenceCollection.read(self.extension_seqs)
result = _make_mini_otu_files(self.key_node,
self.extension_genus_dic_few,
self.extension_seqs)
os.system("rm -r tmp")
self.assertEqual(result, """>P1\nTTAAAAAA\n""")
def test_make_mini_otu_files(self):
os.system("mkdir tmp")
self.extension_seqs = SequenceCollection.read(self.extension_seqs)
result = _make_mini_otu_files(self.key_node,
self.extension_genus_dic_few,
self.extension_seqs)
os.system("rm -r tmp")
self.assertEqual(result, """>P1\nTTAAAAAA\n""")
from qiime_default_reference import get_template_alignment, get_reference_sequences
from skbio import SequenceCollection
gapped_sequences = [
(s.id, str(s)) for s in SequenceCollection.read(get_template_alignment())
][:500]
sequences = [(s.id, str(s))
for s in SequenceCollection.read(get_reference_sequences())][:500]
motif_1 = "GGTGCAAGCCGGTGGAAACA"
def pairwise(l):
res = []
i = iter(l)
for a, b in zip(i, i):
s = min(len(a), len(b))
res.append((a[:s], b[:s]))
return res
def main():
args = handle_program_options()
if osp.isfile(args.out_dir):
print("--out_dir (-o) option must be a valid directory and not a file",
file=sys.stderr)
sys.exit(1)
# will fail gracefully if dir exists
skbu.create_dir(args.out_dir)
metagenomes = []
if args.metagenome_id is not None:
metagenomes.append(args.metagenome_id)
elif args.metagenome_file is not None:
metagenomes.extend(parse_metagenome_file(args.metagenome_file))
if args.verbose:
msg = 'Processing requested for {} metagenome(s) found in: {}'
print(msg.format(len(metagenomes), args.metagenome_file))
# MG-RAST stage.file ids for downloading
derep_passed = '150.1'
screen_passed = '299.1'
for mg_id in metagenomes:
if args.verbose:
print('Processing metagenome: {}'.format(mg_id))
print('\tDownloading: Dereplication Passed...', end='')
sys.stdout.flush()
derepp_rsp = mgapi.mgrast_request('download',
mg_id, {'file': derep_passed},
auth_key=args.auth_key)
derepp_sc = SequenceCollection.read(StringIO(derepp_rsp.text),
format='fastq',
variant='illumina1.8')
if args.verbose:
print('{} sequences'.format(len(derepp_sc)))
print('\tDownloading: Screen Passed...', end='')
sys.stdout.flush()
screenp_rsp = mgapi.mgrast_request('download',
mg_id, {'file': screen_passed},
auth_key=args.auth_key)
screenp_ids = extract_seq_ids(screenp_rsp.text,
fmt='fastq',
variant='illumina1.8')
if args.verbose:
print('{} sequences'.format(len(screenp_ids)))
# filter dereplication passed with IDs from screen passed
failed_screen = filter_seqs(derepp_sc, screenp_ids)
if args.verbose:
nsp = len(screenp_ids)
print(
'\tRemoved {} sequences from Dereplication Passed'.format(nsp))
print('\tleaving {} sequences'.format(len(failed_screen)))
out_fp = osp.join(args.out_dir, mg_id + '_screen_failed.fastq')
failed_screen.write(out_fp, format='fastq', variant='illumina1.8')
if args.verbose:
print('Sequence data written to: ' + out_fp)
from qiime_default_reference import get_template_alignment, get_reference_sequences from skbio import SequenceCollection gapped_sequences = [(s.id, str(s)) for s in SequenceCollection.read(get_template_alignment())][:500] sequences = [(s.id, str(s)) for s in SequenceCollection.read(get_reference_sequences())][:500] motif_1 = "GGTGCAAGCCGGTGGAAACA"
log_choices = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
parser.add_argument(
'--log-level', '-l', default="INFO", choices=log_choices,
help="Set logging level. Default is info."
)
return parser
if __name__ == '__main__':
parser = get_argument_parser()
args = parser.parse_args()
level = getattr(logging, args.log_level.upper(), logging.INFO)
logging.basicConfig(level=level)
sequences = SequenceCollection.read(args.infile, format=args.format)
if args.parallel == 0 and len(sequences) > 16:
pool_size = multiprocessing.cpu_count()
else:
pool_size = 1
dmatrix = create_distance_matrix(sequences, d2.distance, pool_size,
statistic=d2.d2_neighbourhood_dna)
print(dmatrix)
phylo_tree = nj(dmatrix)
print(phylo_tree.ascii_art())
phylo_tree.write(args.outfile, format=args.target)
