/usr/lib/python2.7/dist-packages/biotools/BLAST.py is in python-biotools 1.2.12-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 | #!/usr/bin/env python
'''
A module to manage BLAST databases and interface with the BLAST+ standalone
program available from NCBI.
'''
import biotools.IO as io
import subprocess
from os import sep, getenv, listdir
import shutil
def run(db, sfile, mega_blast=False, **kwargs):
'''
Takes a database and a query and runs the appropriate type of BLAST on
them. The database can be an existing BLAST database or a fasta/fastq
file. If it is a sequence file, this function will look in the places
where BLAST would look for an existing database created from that file and
use that instead. If there is no such database, this function will make
one for you and then use the newly created database with BLAST.
Optional named arguments can currently only be `evalue`, `num_threads`,
`gapopen`, or `gapextend`. The correspond to the BLAST options of the same
name.
'''
cmds = {
'prot': {
'prot': 'blastp',
'nucl': 'tblastn'
},
'nucl': {
'nucl': 'blastn',
'prot': 'blastx'
}
}
seq = io.open(sfile, 'r').next()
qtype = seq.type
rcloc = ''
for loc in (".:~:" + (getenv("NCBI") or "")).split(':'):
if loc and loc[-1] == sep:
loc += sep
try:
for line in (l.strip() for l in open(loc + '.ncbirc', 'r')):
pos = line.find('=')
if pos >= 0 and line[:pos].strip() == "BLASTDB":
rcloc = line[pos + 1:].strip()
except IOError:
pass
dbtype = None
bdbenv = getenv("BLASTDB")
dblocations = (":." + ((':' + bdbenv) if bdbenv else '') +
((':' + rcloc) if rcloc else '')).split(':')
for loc in dblocations:
if loc and loc[-1] != sep:
loc += sep
try:
open(loc + db + '.pin', 'r')
dbtype = 'prot'
break
except IOError:
try:
open(loc + db + '.nin', 'r')
dbtype = 'nucl'
break
except IOError:
pass
if not dbtype:
odb = db
pos = db.rfind(".")
for seq in io.open(db, 'r'):
dbtype = seq.type
break
if not dbtype:
raise IOError("Database not found: " + odb)
ndb = None
sp = db.rfind(sep)
if sp > -1:
dbdir, db = db[:sp], db[sp + 1:pos]
else:
dbdir, db = '.', db[:pos]
for file in listdir(dbdir):
dpos = file.rfind('.')
if dpos >= 0 and file[dpos + 1:] == dbtype[0] + 'in':
fh = open(dbdir + sep + file, 'r')
c = ord(fh.read(12)[-1])
fname = fh.read(c)
if fname[0] in ("'", '"'):
fname = fname[1:-1]
if fname.endswith(odb):
ndb = dbdir + sep + file[:dpos]
break
if not ndb:
ndb = '_'.join(db.split())
try:
ignore = open('/dev/null', 'w')
except IOError:
ignore = open('nul', 'w')
try: # possible race condition
open(ndb, 'r').close()
except IOError:
subprocess.call(["makeblastdb", "-in", '"%s"' % odb,
"-out", ndb, "-dbtype", dbtype],
stdout=ignore)
try:
for suff in ['in', 'hr', 'sq']:
name = ndb + '.' + dbtype[0] + suff
shutil.move(name, dbdir + sep + name)
except shutil.Error:
pass
db = dbdir + sep + ndb
else:
db = ndb
else:
raise IOError("Database not found: " + db)
allowed = set(["evalue", "gapopen", "gapextend", "num_threads"]) & \
set(kwargs.keys())
cmd = cmds[qtype][dbtype]
pn = ["-db", "-query"]
if mega_blast:
cmd = "megablast"
pn = ["-d", "-i"]
allowed = ["e", "a"]
args = [cmd, pn[0], db, pn[1], sfile] + [arg for pair in
[["-" + k, str(kwargs[k])] for k in allowed] for arg in pair]
proc = subprocess.Popen(args, bufsize=1, stdout=subprocess.PIPE)
return Result(iter(proc.stdout.readline, ''))
class Result(object):
'''
A class which take the raw output from BLAST and generates dictionaries
from the data from BLAST. This data includes the alignment, percent
identity, gaps, e-value, score, length of subject, length of query, and
start and stop positions for both sequences. This class should be used in
a for loop like so:
```python
for res in Result(file_or_data):
pass
```
The class instance has a single other property, `headers`, which are the
lines in BLAST results before the BLAST hits (e.g., citation info, etc.).
'''
def __init__(self, file):
self.file = file
self.headers = []
def __iter__(self):
try:
ipt = open(self.file, 'r')
except (IOError, TypeError):
try:
ipt = self.file.split('\n')
except:
ipt = self.file
mode = 0
headers = []
curr = None
length = 0
def sh(sn, qn, l):
qdl = ''
space = qn.find(' ')
if space > -1:
qn, qdl = qn[:space], qn[space + 1:].lstrip()
return {
'subject': {
'name': sn.lstrip(),
'defline': '',
'start': None,
'end': None,
'sequence': ''
},
'query': {
'name': qn,
'defline': qdl,
'start': None,
'end': None,
'sequence': ''
},
'length': l
}
def ra(sh):
for res in ('subject', 'query'):
sh[res]['start'] = int(sh[res]['start'])
sh[res]['end'] = int(sh[res]['end'])
sh[res]['length'] = abs(sh[res]['end'] - sh[res]['start'] + 1)
return sh
def sh_fmt(l):
for pairs in (a.strip() for a in l.split(',')):
l, r = tuple(a.strip() for a in (pairs.split('=')[:2]
if '=' in pairs else pairs.split(':')[:2]))
subheaders[l.lower().split('(')[0]] = r
for line in ipt:
line = line.rstrip('\n').lstrip()
if not line:
if mode == 4:
mode = 5
continue
if mode == 0:
if line[:6] == 'Query=':
mode = 1
qname = line[6:].lstrip()
self.headers = headers
else:
headers.append(line)
elif mode == 1:
if line[0] == '>':
mode = 3
subheaders = sh(line[1:], qname, length)
elif line[:7] == 'Length=':
length = int(''.join(line[7:].strip().split(',')))
mode = 2
elif line[0] == '(' and line.endswith('letters)'):
length = int(''.join(line[1:-8].strip().split(',')))
mode = 2
elif line[:6] == 'Query=':
qname = line[6:].lstrip()
else:
qname += line
elif mode == 2:
if line[0] == '>':
mode = 3
subheaders = sh(line[1:], qname, length)
elif line[:6] == 'Query=':
qname = line[6:].lstrip()
mode = 1
elif mode == 3:
if line[:5] == 'Score':
snm = subheaders['subject']['name']
defline = ''
space = snm.find(' ')
if space > -1:
snm, defline = snm[:space], snm[space + 1:]
subheaders['subject']['name'] = snm
subheaders['subject']['defline'] = defline
sh_fmt(line)
mode = 4
elif line[:7] == 'Length=':
pass
elif line[0] == '(' and line.endswith('letters)'):
pass
else:
subheaders['subject']['name'] += line
elif mode == 4:
sh_fmt(line)
elif mode == 5:
if line[:6] == 'Query=':
mode = 1
qname = line[6:].lstrip()
yield ra(subheaders)
continue
elif line[0] == '>':
yield ra(subheaders)
subheaders = sh(line[1:], qname, length)
mode = 3
continue
elif line[:5] == 'Score':
yield ra(subheaders)
subheaders = sh(subheaders['subject']['name'], qname,
length)
sh_fmt(line)
mode = 4
continue
elif line[:5] == 'Sbjct':
curr = 'subject'
elif line[:5] == 'Query':
curr = 'query'
else:
continue
_, start, seq, end = line.split()
subheaders[curr]['start'] = subheaders[curr]['start'] or start
subheaders[curr]['end'] = end
subheaders[curr]['sequence'] += seq
try:
yield ra(subheaders)
except UnboundLocalError:
pass
raise StopIteration()
if __name__ == '__main__':
import sys
if len(sys.argv) > 1:
output = open(sys.argv[1]).read()
for result in Result(output):
print(result)
|