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import pkg_resources
import tempfile
import magic
import subprocess
import tempfile
import logging
import re
import io
import gzip
log = logging.getLogger(__name__ )
def read_fasta(sequence):
entries = 0
bases = []
label = None
for line in sequence:
if line.startswith(">"):
label = line
entries += 1
else:
bases.append(line)
if entries > 1:
log.debug("FASTA file contains multiple entries")
raise ValueError("FASTA file contains multiple entries")
return label, bases
def qc_fasta(arg_sequence):
log.debug("Starting qc_fasta")
schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
with tempfile.NamedTemporaryFile() as tmp:
tmp.write(schema_resource.read())
tmp.flush()
val = magic.Magic(magic_file=tmp.name,
uncompress=False, mime=True)
gz = ""
if arg_sequence.name.endswith(".gz"):
sequence = gzip.GzipFile(fileobj=arg_sequence, mode='rb')
gz = ".gz"
else:
sequence = arg_sequence
sequence = io.TextIOWrapper(sequence)
r = sequence.read(4096)
sequence.seek(0)
seqlabel = r[1:r.index("\n")]
seq_type = val.from_buffer(r).lower()
if seq_type == "text/fasta":
# ensure that contains only one entry
submitlabel, submitseq = read_fasta(sequence)
with tempfile.NamedTemporaryFile() as tmp1:
refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
tmp1.write(refstring)
tmp1.write(submitlabel.encode("utf8"))
tmp1.write(("".join(submitseq)).encode("utf8"))
tmp1.flush()
subbp = 0
refbp = 0
similarity = 0
try:
cmd = ["clustalw", "-infile="+tmp1.name,
"-quicktree", "-iteration=none", "-type=DNA"]
print("QC checking similarity to reference")
print(" ".join(cmd))
result = subprocess.run(cmd, stdout=subprocess.PIPE)
res = result.stdout.decode("utf-8")
g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
refbp = float(g1.group(1))
g2 = re.search(r"^Sequence 2: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
subbp = float(g2.group(1))
g3 = re.search(r"^Sequences \(1:2\) Aligned\. Score: (\d+(\.\d+)?)$", res, flags=re.MULTILINE)
similarity = float(g3.group(1))
print(g1.group(0))
print(g2.group(0))
print(g3.group(0))
except Exception as e:
logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
if refbp and (subbp/refbp) < .7:
raise ValueError("QC fail: submit sequence length is shorter than 70% reference")
if refbp and (subbp/refbp) > 1.3:
raise ValueError("QC fail: submit sequence length is greater than 130% reference")
if similarity and similarity < 70.0:
raise ValueError("QC fail: submit similarity is less than 70%")
if refbp == 0 or similarity == 0:
raise ValueError("QC fail")
return ("sequence.fasta"+gz, seqlabel)
elif seq_type == "text/fastq":
return ("reads.fastq"+gz, seqlabel)
else:
raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")
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