forked from zheminzhou/KleTy
-
Notifications
You must be signed in to change notification settings - Fork 1
/
amrsearch.py
232 lines (209 loc) · 10.1 KB
/
amrsearch.py
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
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
import os, click, pandas as pd, numpy as np, re
from Bio import Seq
try :
from uberBlast import uberBlast, readFastq
from configure import dbs
except :
from .uberBlast import uberBlast, readFastq
from .configure import dbs
resfams = dbs['resfams']
dbs = dbs['amr_dbs']
def get_tops(bsn) :
bsn = bsn[np.argsort(-bsn.T[11]*bsn.T[3]/bsn.T[12])]
covs = { c:[] for c in np.unique(bsn.T[1]) }
for p in bsn :
s, e = p[8:10] if p[8] < p[9] else (p[9], p[8])
x = np.zeros(e-s+1, dtype=np.uint8)
for c in covs[p[1]] :
if c[0] > e or c[1] < s :
continue
ovl = [max(c[0], s), min(c[1], e)]
if ovl[1] - ovl[0] + 1 >= 0.3 * (c[1] - c[0] + 1) :
p[1] = ''
break
x[ovl[0]-s:ovl[1]-s+1] = 1
if np.sum(x) >= 0.3 * (e - s + 1) :
p[1] = ''
break
else :
covs[p[1]].append([s, e])
return bsn[bsn.T[1] != '']
def rc(s) :
c = {'A':'T', 'T':'A', 'G':'C', 'C':'G', '-':'-'}
return ''.join([ c.get(x, 'N') for x in s[::-1].upper() ])
def amrsearch(query, g_table=11, n_proc=8) :
bla_category = {}
if os.path.isfile(resfams) :
with open(resfams, 'rt') as fin :
for line in fin :
p = line.strip().split('|')
variant = p[4]
if variant in bla_category :
continue
func, t = [], p[7]
if 'carbapenem' in t :
func.append('CARBAPENEM')
if 'extended-spectrum' in t :
func.append('ESBL')
if 'inhibitor-resistant' in t or 'metallo-' in t :
func.append('INHIBITOR-RESISTANT')
if len(func) :
bla_category[variant] = func
qry, _ = readFastq(query)
res = []
resistance = {}
for title, (db, site, min_iden, min_cov) in dbs.items() :
if title.startswith('prot') :
bsn = uberBlast('-r {0} -q {1} -f --diamondx --min_id {2} --min_ratio {3} -t {4} -p -s 2 -e 0,3 -m --merge_gap 300'.format(
query, db, min_iden/100., min_cov/100., n_proc).split())
if title == 'prot' :
for p in bsn :
ref = p[0].split(' ')[0].split('|')
if ref[6] != 'mutation' :
resistance[ref[4]] = ref[8:10]
resistance[ref[5]] = ref[8:10]
else :
bsn = uberBlast('-r {0} -q {1} -f --blastn --min_id {2} --min_ratio {3} -t {4} -p -s 2 -e 0,3 -m --merge_gap 300'.format(
query, db, min_iden/100., min_cov/100., n_proc).split())
bsn = get_tops(bsn)
if site == None :
for p in bsn:
if title == 'nucl' :
ref = p[0].split(' ')[0].split('|')
category = ''
elif title == 'nuc_vir' :
if p[0].find('delete') >= 0 :
continue
if p[0].find('__rmp') >= 0 :
p[0] = re.split('__', p[0])[2]
x = p[0].rsplit('_', 1)[0]
ref = ['', p[0], '', '', '', p[0], x, x, x]
category = p[0][:3]
if category in ('fyu', 'irp') :
category = 'ybt'
elif category in ('iut') :
category = 'iuc'
elif title.endswith('plasmids') :
x = p[0].rsplit('|', 1)[-1]
ref = ['', p[0], '', '', '', x, x, x, x]
category = 'MOB_TYPE' if x.startswith('MOB') else ('MPF_TYPE' if x.startswith('MPF') else 'INC_TYPE')
else :
x = p[0].rsplit('_', 1)[0]
ref = ['', p[0], '', '', '', p[0], x, x, x]
category = p[0][:3]
qry_na = Seq.Seq(qry[p[1]][p[8]-1:p[9]]) if p[8] < p[9] else Seq.Seq(qry[p[1]][p[9]-1:p[8]]).reverse_complement()
if title == 'nuc_plasmids' :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5], ref[6], category, category, ref[7]])
elif title == 'prot_plasmids' :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5], ref[6], category, category, ref[7]])
elif (abs(p[9] - p[8]) + 1) % 3 > 0 :
if (max([len(x) for x in qry_na[:int((len(qry_na))/3)*3].translate(g_table).split('*')])*3) >= 0.85 * len(qry_na) or \
(max([len(x) for x in qry_na[len(qry_na)%3:].translate(g_table).split('*')])*3) >= 0.85 * len(qry_na) :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5], ref[6], category, category, ref[7]])
else :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5] + '(*Frameshift)', ref[6], category, category, ref[7]])
else :
qry_aa = qry_na.translate(g_table)
if '*' in qry_aa[:-1] and max([len(x) for x in qry_aa.split('*')])*3 < 0.85 * len(qry_na) :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5] + '(*Premature)', ref[6], category, category, ref[7]])
else :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTN', ref[5], ref[6], category, category, ref[7]])
else :
sites = pd.read_csv(site, sep='\t').values[:, -6:]
for p in bsn :
ref = p[0].split(' ')[0].split('|')
if len(ref) > 1 :
if ref[6] != 'mutation' :
res.append([p[1], p[8], p[9], p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), ref[1], 'BLASTX', ref[4], ref[5], ref[8], ref[9], ref[10]])
ref = ref[1:]
psite = {}
for x in sites[sites.T[0] == ref[0]] :
loc = int(x[1])
if loc >= p[6] and loc <= p[7] :
variation = list(re.findall(r'_([^-\d]+)[-\d]+([^-\d]+)', x[2])[0])
if variation[1].upper() == 'DEL' :
variation[1] = '-' * len(variation[0])
elif variation[1].upper() == 'STOP' :
variation[1] = '*'
if len(variation[0]) > len(variation[1]) :
variation[1] += '-' * (len(variation[0]) - len(variation[1]))
elif len(variation[1]) > len(variation[0]) :
variation[0] += '-' * (len(variation[1]) - len(variation[0]))
psite[loc] = [x, variation]
if len(psite) < 1 :
continue
qry_s = Seq.Seq(qry[p[1]][p[8]-1:p[9]]) if p[8] < p[9] else Seq.Seq(qry[p[1]][p[9]-1:p[8]]).reverse_complement()
cigar = [[int(s), t] for s, t in re.findall('(\d+)([MID])', p[14])]
if title == 'prot' :
mv = 3
qry_s = qry_s.translate(g_table)
cigar = [ [int(s/3), t] for s, t in cigar ]
else :
mv = 1
c = 0
qq = []
for s, t in cigar :
if t != 'I' :
qq.append(str(qry_s[c:c+s]))
c += s
else :
qq.append('-' * s)
qq = ''.join(qq)
ss = ''.join([ (t * s) if t != 'D' else ('-'*s) for s, t in cigar ])
if p[8] > p[9] :
mv *= -1
qi, ri = p[8] - mv, p[6] - 1
for xi, (q, r) in enumerate(zip(list(qq), list(ss))) :
if q != '-' :
qi += mv
if r != '-' :
ri += 1
if ri in psite :
x, variation = psite.pop(ri)
bq = qq[xi:xi+len(variation[1])]
if bq == variation[1] :
len_v = len(variation[1].replace('-', ''))
len_x = 1 if p[8] > p[9] else -1
res.append([p[1], qi, qi+mv*len_v+len_x, p[2]*100, np.round(100.*(p[7]-p[6]+1)/p[12], 2), x[0], 'MUTATION', x[2], x[2].split('_', 1)[0], x[4], x[3], x[5]])
if len(psite) < 1 :
break
# import datetime
# dt_string = datetime.datetime.now().strftime("%d/%m/%Y %H:%M:%S")
# print(title, dt_string)
for r in res :
if r[9] == '' :
if r[7] in resistance :
r[9:11] = resistance.get(r[7], ['', ''])
else :
r[9:11] = resistance.get(r[8], ['', ''])
if r[7] in bla_category :
r[9] = '/'.join( sorted(set(r[9].split('/')+bla_category[r[7]])) )
res = sorted([ r for r in res if r[9] != '' ])
for j, r2 in list(enumerate(res))[1:] :
todel = []
for r1 in res[j-1::-1] :
if r1[0] == '' :
continue
if r1[0] != r2[0] :
break
s1, e1 = sorted(r1[1:3])
s2, e2 = sorted(r2[1:3])
ovl = min(e2, e1) - max(s1, s2) + 1
if ovl >= 0.5 * (e1-s1+1) or ovl >= 0.5 * (e2-s2+1) :
sc1 = (e1-s1+1) * r1[3] * r1[4]/10000.
sc2 = (e2-s2+1) * r2[3] * r2[4]/10000.
if sc1 >= sc2 :
r2[0] = ''
break
else :
todel.append(r1) #r1[0] = ''
if r2[0] != '' :
for r1 in todel :
r1[0] = ''
return [r for r in res if r[0] != '']
@click.command()
@click.option('-q', '--query')
def main(query) :
amrsearch(query)
if __name__ == '__main__' :
main()