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
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
|
import sys
import os
import time
import toolshed as ts
files = [
dict(file="ESP6500SI.all.snps_indels.tidy.v2.vcf.gz",
fields=["EA_AC", "AA_AC"],
names=["esp_ea", "esp_aa"],
ops=["first", "first"]),
dict(file="ExAC.r0.3.sites.vep.tidy.vcf.gz",
fields=["AC_Adj", "AC_Het", "AC_Hom", "AC_NFE"],
names=["exac_AC_Adj", "exac_AC_Het", "exac_AC_Hom", "exac_AC_NFE"],
ops=["first", "first", "first", "first"]),
dict(file="hg19_fitcons_fc-i6-0_V1-01.bed.gz",
columns=[4],
names=["fitcons_mean"],
ops=["mean"],
h="fitcons.hdr",
c="CHROM,FROM,TO,FITCONS"),
dict(file="ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz",
fields=["EAS_AF", "AMR_AF"],
names=["1kg_eas_af", "1kg_amr_af"],
ops=["first", "first"]),
dict(file="GRCh37-gms-mappability.vcf.gz",
fields=["GMS_illumina"],
names=["gms_mappapility"],
ops=["first"]),
dict(file="clinvar_20150305.tidy.vcf.gz",
fields=["CLNHGVS"],
names=["clinvar_hgvs"],
ops=["first"]),
dict(file="cosmic-v68-GRCh37.tidy.vcf.gz",
fields=["ID"],
names=["cosmic_id"],
ops=["concat"]),
dict(file="dbsnp.b141.20140813.hg19.tidy.vcf.gz",
fields=["RS"],
names=["dbsnp_id"],
ops=["concat"]),
dict(file="hg19.gerp.elements.bed.gz",
columns=[4],
names=["gerp"],
ops=["mean"],
h="gerp.hdr",
c="CHROM,FROM,TO,GERP"),
]
def get():
base = "http://s3.amazonaws.com/gemini-annotations/"
try:
os.mkdir("data")
except OSError:
pass
for f in files:
f = f['file']
if not (os.path.exists("data/" + f) and os.path.exists("data/" + f + ".tbi")):
cmd = ("|wget -O tmp.tt.gz {base}{f} && sleep 2 && ./vcfsort.sh tmp.tt.gz | bgzip -c > data/{f} && sleep 2 && tabix -f data/{f}; rm -f tmp.tt.gz".format(**locals()))
list(ts.nopen(cmd))
get()
def asanno(d):
c = "fields={fields}" if "fields" in d else "columns={columns}"
tmpl = """
[[annotation]]
file="{file}"
names={names}
ops={ops}
""" + c + "\n"
return tmpl.format(**d)
def asbcf(d):
d['cols'] = "+" + ",+".join(d['fields']) if 'fields' in d else d["c"]
d['hdr'] = "-h " + d['h'] if 'h' in d else ""
return 'bcftools annotate -a {DATA}/{file} -c "{cols}" {hdr}'.format(**d)
with open('fitcons.hdr', 'w') as fh:
fh.write('##INFO=<ID=FITCONS,Number=1,Type=Float,Description="FITCONS VALUE">\n')
with open('gerp.hdr', 'w') as fh:
fh.write('##INFO=<ID=GERP,Number=1,Type=Float,Description="GERP VALUE">\n')
toml = "compare.toml"
with open(toml, "w") as fh:
for d in files:
fh.write(asanno(d))
DATA = 'data'
QUERY = "data/ExAC.r0.3.sites.vep.tidy.vcf.gz"
for f in files:
f['DATA'] = DATA
f['QUERY'] = QUERY
commands = [asbcf(f) for f in files]
query = QUERY.format(DATA=DATA)
fnames = [f['DATA'] + "/" + f['file'] for f in files]
bedtools_cmd = ("bedtools intersect -sorted -sortout -wao -a {query} -b " + " -b ".join(fnames)).format(query=query)
# TODO: send to file to match bcftools and vcfanno
fh = open("timing.txt", "w")
print >>fh, "method\ti\tseconds\tprocs"
t = time.time()
list(ts.nopen("|%s | bgzip -c > /tmp/trash.gz" % bedtools_cmd))
print >>fh, "bedtools\t%d\t%.2f\t1" % (len(commands), time.time() - t)
for procs in (1, 4, 8, 12):
if procs == 1:
tottime = 0
for i in range(len(commands)):
out = "tmp%d.vcf.gz" % i
try:
os.unlink("tmp%d.vcf.gz" % (i - 2))
except OSError:
pass
query = QUERY.format(DATA=DATA) if i == 0 else ("tmp%d.vcf.gz" % (i - 1))
cmd = commands[i] + " {query} | bgzip -c > {out}; tabix {out} ".format(DATA=DATA, query=query, out=out)
print >>sys.stderr, cmd
t = time.time()
res = list(ts.nopen("|%s" % cmd))
t1 = time.time()
tottime += t1 - t
print >>fh, "bcftools\t%d\t%.2f\t1" % (i+1, tottime)
sys.stdout.flush()
vcmd = "vcfanno -p {procs} -base-path {DATA} {toml} {QUERY} | bgzip -c > /dev/null".format(
DATA=DATA, procs=procs, QUERY=QUERY, toml=toml)
print >>sys.stderr, vcmd
#print vcmd
t = time.time()
res = list(ts.nopen("|%s" % vcmd))
t1 = time.time()
print >>fh, "vcfanno\t%d\t%.2f\t%d" % (i+1, t1 - t, procs)
|
