def test_sbol(self):
# feat = os.path.join(TEST_DATA, 'pEGBAn11.gb')
# print feat.genbank_file
seq = read(os.path.join(TEST_DATA, 'pEGBAn11.gb'), 'gb')
fhand = open('/tmp/sbol.xml', 'w')
fhand.write(convert_to_sbol(seq))
fhand.close()
def test_single_contig(self):
record = read(fspath(self.data / "U00096-3.fasta"), "fasta")
with (self.data / "U00096-3.fasta.chopped.fasta").open() as f:
expected = list(parse(f, "fasta"))
with tempfile.NamedTemporaryFile(mode="rt", suffix=".fna") as tmp:
orthoani._chop(record, tmp.name, 1020)
actual = list(parse(tmp, "fasta"))
for actual_record, expected_record in zip(actual, expected):
self.assertEqual(actual_record.seq, expected_record.seq)
def reference(ctx, verbose, primer_begin, primer_end, start_codon, end_codon,
reference, input, output):
numeric_level = get_verbosity_level(verbose)
logging.basicConfig(level=numeric_level)
click.echo("Creating reference library with primer {}{}-->{}{}".format(
primer_begin, start_codon * "N", end_codon * -1 * "N", primer_end))
reference_seq = str(read(reference, "fasta").seq)
reference_library = ReferenceLibrary(primer_begin, primer_end,
reference_seq, start_codon, end_codon)
reference_library.apply(input)
reference_library.to_json(output)
def feature_sbol(request, uniquename):
user = request.user
print(uniquename)
try:
feat = Feature.objects.get(uniquename=uniquename)
except Feature.DoesNotExist:
feat = None
if feat is None:
return Http404
if (feat.is_public or (user.is_staff or user == feat.owner)):
seq = read(feat.genbank_file, 'gb')
response = HttpResponse(convert_to_sbol(seq), content_type='xml/plain')
filename = seq.name + '.xml'
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}"'.format(filename)
return response
else:
return HttpResponseForbidden
matrix_file = arguments['--matrix']
with open(matrix_file, 'r') as matrix_file:
matrice_dict = substitution_matrices.read(matrix_file)
aligner.substitution_matrix = matrice_dict
else:
aligner.match_score = int(arguments['--matchscore'])
aligner.mismatch_score = int(arguments['--mismatchscore'])
aligner.open_gap_score = int(arguments['--opengapscore'])
aligner.extend_gap_score = int(arguments['--extendgapscore'])
out_file = arguments['-o']
input_file_format = arguments['--informat']
if len(input_files) == 2:
sequences = [
read(input_file, input_file_format) for input_file in input_files
]
first = sequences[0]
second = sequences[1]
elif len(input_files) == 1:
sequences = parse(input_files[0], input_file_format)
first = next(sequences)
second = next(sequences)
else:
raise (RuntimeError(
'Please provide exactly 1 or 2 sequences in each file'))
score = aligner.score(first.seq, second.seq)
print(f'Maximum score: {score}')
alignments = aligner.align(first.seq, second.seq)
with open(out_file, 'w') as out_file:
info = {
"resistance": resistance,
# "name": id_,
"id": id_,
# "type": type_,
"location": row.find("b").text.strip().replace(" / ", ""),
"addgene_id": row.find("a").get("href").strip("/"),
}
# get the ZIP sequence
for path in ("{} cor.gbk", "{}.gbk", "{}.gb"):
if archive.exists(path.format(id_)):
break
with archive.open(path.format(id_), encoding="latin-1") as f:
rec = f.read().replace("Exported File", "Exported ")
gb_archive = CircularRecord(read(six.StringIO(rec), "gb"))
# get the AddGene sequences page
url = "https://www.addgene.org/{}/sequences/".format(info["addgene_id"])
with session.get(url) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
# get the addgene full sequence
gb_url = soup.find("a", class_="genbank-file-download").get("href")
with requests.get(gb_url) as res:
gb = info["gb"] = CircularRecord(read(io.StringIO(res.text), "gb"))
if id_ == "pICSL30008":
gb = gb.reverse_complement(True, True, True, True, True, True, True)
# elif id_ == "pICSL50004":
# gb_archive = gb_archive.reverse_complement(True, True, True, True, True, True, True)
def setUpClass(cls):
cls.data = pathlib.Path(__file__).parent / "data"
cls.r1, cls.r2 = map(lambda p: read(fspath(p), "fasta"),
cls.data.glob("1852379.*.fna"))
def main():
seq = read(sys.argv[1], 'fasta')
qual = read(sys.argv[2], 'qual')
seq.letter_annotations = qual.letter_annotations
write(seq, sys.stdout, 'fastq')
# "type": type_,
"location": row.find("b").text.strip().replace(" / ", ""),
"addgene_id": row.find("a").get("href").strip("/"),
}
# get the online full sequence
if id_ in FULL_SEQUENCES:
# Load the AddGene sequences page and get the full sequence
with requests.get(FULL_SEQUENCES[id_]) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
section = soup.find("section", id="depositor-full")
gb_url = soup.find("a",
class_="genbank-file-download").get('href')
# Get the Genbank file
with requests.get(gb_url) as res:
gb = CircularRecord(read(io.StringIO(res.text), "gb"))
# get the pBP-SJM901 sequence and patch it
elif id_.startswith("pBP-SJM"):
# get pBP-SJM
# Load the AddGene sequences page and get the full sequence
with requests.get(FULL_SEQUENCES["pBP-SJM901"]) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
section = soup.find("section", id="depositor-full")
gb_url = soup.find("a",
class_="genbank-file-download").get('href')
# Get the Genbank file
with requests.get(gb_url) as res:
gb = CircularRecord(read(io.StringIO(res.text), "gb"))
# replace the target sequence
gb.seq = Seq(
# Update the progress bar
it.set_description(id_)
# extract info
info = {
"resistance": resistance,
# "name": id_,
"id": id_,
# "type": type_,
"location": row.find("b").text.strip().replace(" / ", ""),
"addgene_id": row.find("a").get("href").strip("/"),
}
# get the ZIP sequence
with archive.open("{}.gb".format(id_)) as f:
gb_archive = CircularRecord(read(f, "gb"))
pref, _ = BB_PREFIX.search(gb_archive).span()
gb_archive <<= pref - 1
# get the AddGene sequences page
url = "https://www.addgene.org/{}/sequences/".format(
info["addgene_id"])
with session.get(url) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
# No full sequence available, but it's actually almost the same
# as DVK_EF, so we can simply patch the sequence and it will be
# fine
if id_ in ("DVK_AE", "DVK_AF"):
# Load the DVK_EF page and find the GenBank file link
"location": row.find("b").text.strip().replace(" / ", ""),
"addgene_id": row.find("a").get("href").strip("/"),
}
# get the AddGene sequences page
url = "https://www.addgene.org/{}/sequences/".format(
info["addgene_id"])
with session.get(url) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
# get the addgene full sequence
section = soup.find("section", id="addgene-full")
gb_url = section.find("a", class_="genbank-file-download").get("href")
with requests.get(gb_url) as res:
gbd = info["gb_depositor"] = CircularRecord(
read(io.StringIO(res.text), "gb"))
# get the AddGene plasmid page
url = "https://www.addgene.org/{}/".format(info["addgene_id"])
with session.get(url) as res:
soup = bs.BeautifulSoup(res.text, "html.parser")
# get the deposited record
section = soup.find("ul", class_="addgene-document-list")
gb_url = section.find("a").get("href")
with requests.get(gb_url) as res:
gba = info["gb_addgene"] = CircularRecord(
read(io.StringIO(res.text), "gb"))
# Sanity check
if len(gba) != len(gbd):
