/usr/lib/python3/dist-packages/biotools/BLAST.py is in python3-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.
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'''
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)
|