1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
|
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, check_with_mimimap2=True):
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)
sequence.seek(0)
sequence.detach()
if check_with_mimimap2:
with tempfile.NamedTemporaryFile() as tmp1:
with tempfile.NamedTemporaryFile() as tmp2:
refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
tmp1.write(refstring)
tmp1.flush()
tmp2.write(submitlabel.encode("utf8"))
tmp2.write(("".join(submitseq)).encode("utf8"))
tmp2.flush()
similarity = 0
try:
cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
logging.info("QC checking similarity to reference")
logging.info(" ".join(cmd))
result = subprocess.run(cmd, stdout=subprocess.PIPE)
result.check_returncode()
res = result.stdout.decode("utf-8")
mm = res.split("\t")
if len(mm) >= 10:
# divide Number of matching bases in the mapping / Target sequence length
similarity = (float(mm[9]) / float(mm[6])) * 100.0
else:
similarity = 0
except Exception as e:
logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e)
if similarity < 70.0:
raise ValueError(
"QC fail for {}: alignment to reference was less than 70%% (was %2.2f%%)".format(
seqlabel, similarity
))
return "sequence.fasta" + gz, seqlabel, seq_type
elif seq_type == "text/fastq":
sequence.seek(0)
sequence.detach()
return "reads.fastq" + gz, seqlabel, seq_type
else:
raise ValueError("Sequence file ({}) does not look like a DNA FASTA or FASTQ".format(arg_sequence))
|
