def target():
while 1:
try:
res = qin.get(PIPING, 1)
except queue.Empty:
if not PIPING:
break
else:
continue
qname, sname = res['query']['name'], res['subject']['name']
start, end = res['query']['start'], res['query']['end']
alignments = []
max_match = (options.MIN_IDENTITY, None)
if subj[sname].type == 'nucl':
subject = translate(subj[sname])
else:
subject = subj[sname]
while qname:
try:
o = orfs[qname]
break
except KeyError:
qname = qname[:-1]
if not qname:
qin.task_done()
continue
for orf in o:
if in_range(orf, start, end, 0):
orf = orf[:-3]
query = translate(orf)
options.debug("Aligning %33s v. %33s." % (qname, sname))
alignment = align(subject.seq, query.seq)
alignments.append((orf, sname, alignment))
for orf, refname, aln in alignments:
hitlen = aln['sublength']
region = orf[-3 * hitlen:]
identity = float(aln['identities']) / aln['length']
if identity >= max_match[0]:
max_match = (identity, (region, sname, aln))
if max_match[1]:
seq, name, _ = max_match[1]
odl = subject.defline.split('[')[0].strip()
src = seq.original.name
start, end, strand = seq.start, seq.end, seq.step
defline = '%s[source=%s] [start=%d] [end=%d] [strand=%d]' % \
(odl + (' ' if odl else ''), src, start, end, strand)
new = Sequence(name.strip(), seq.seq, defline=defline,
original=seq.original, type=seq.type,
start=seq.start, end=seq.end, step=seq.step)
qout.put(new)
qin.task_done()
def var(files):
'''
Returns plot data and metadata for plotting later on in the pipeline.
'''
sort = {}
for f in files:
seqs = [s for s in io.open(f)]
type = set(s.type for s in seqs)
if len(type) > 1:
type = set(['prot'])
fid = (type.pop(), f)
seqs = [''.join(s.seq.split('-')).strip() for s in seqs]
seqs = [translate(s) if fid[0] == 'nucl' else s for s in seqs]
sset = frozenset(seqs)
srtr = (len(seqs), sset)
sort[srtr] = sort.get(srtr, set()) | set([fid])
couples = []
for partners in sort.values():
trim = lambda x: '.'.join(x.split('.')[:-1]) \
if f.endswith('.clustalw') or \
f.endswith('.clustal') or \
f.endswith('.aln') else x
names = ', '.join(set(trim(f.split(sep)[-1]) for type, f in partners))
pair = {}
for type, f in partners:
if len(pair) == 2:
break
if type in pair:
continue
pair[type] = f
if 0 < len(pair) < 2:
raise TypeError("Unmatched clustal alignment(s): " +
", ".join(f for type, f in partners))
if len(pair) == 0:
continue
couples.append((pair['nucl'], pair['prot'], names))
for nt, aa, strain in couples:
plotdata = {
'nt': SaySNPs(nt),
'aa': SaySNPs(aa)
}
metadata = {'strain': strain, 'filename': strain + '.pdf'}
yield {'plotdata': plotdata, 'metadata': metadata}
raise StopIteration
def run_clustal():
while not q.empty():
cid = q.get()
dig = hashlib.md5()
dig.update(' '.join(cid))
dig = dig.hexdigest()
fpre = direc + 'nt' + sep + dig
apre = direc + 'aa' + sep + dig
fname = fpre + ".fasta"
aname = apre + ".fasta"
fh = io.open(fname, 'w')
ah = io.open(aname, 'w')
for ipt in clusters:
counter = 0
name = '_'.join(ipt.split(sep)[-1].split('.')[0].split())
for cluster in clusters[ipt]:
if cid & cluster[0]:
nm = name + '_' + str(counter)
seq = cluster[1]
curr = sequ.Sequence(nm, seq, defline=', '.join(cid))
tr = tran.translate(curr)
tr.name = curr.name
fh.write(curr)
ah.write(tr)
counter += 1
fh.close()
ah.close()
try:
clustal.run(fname, fpre + '.clustalw')
clustal.run(aname, apre + '.clustalw')
filenames.append(dig + '.fasta')
except ValueError:
pass
q.task_done()
def OptimalCTether(reference, translation, extend=1, create=10):
'''
This function will take two sequences: a `reference` sequence and another
protein sequence (`translation`; usually, this is an open reading frame
that has been translated). Needleman-Wunsch alignment will be performed
and the substring of translation with the highest identity that begins
with a start codon [default: `['ATG']`] is reported.
This function returns a dictionary of relevent information from the
alignment; specifically, the alignments itself [keys: `query`, `subject`],
the score [key: `score`], the length of the alignment [key: `length`], the
length of the substring of translation used [key: `sublength`], the number
of identities [key: `identities`], and the number of gaps [key: `gaps`].
'''
starts = set(translate(s) for s in options.START_CODONS)
v, w = reference, translation
try:
v = v.seq
except AttributeError:
pass
try:
w = w.seq
except AttributeError:
pass
if not starts & set(w):
raise ValueError("Open reading frame does not contain a start codon.")
v, w = v[::-1], w[::-1]
lv, lw = len(v), len(w)
rv, rw = range(lv + 1), range(lw + 1)
gpc = [[create * int(not (i | j)) for i in rw] for j in rv]
mat = [[-(i + j) * extend - create * (not (i | j) and w[0] != v[0])
for i in rw] for j in rv]
pnt = [[VGAP_MARK if i > j else HGAP_MARK if j > i else DIAG_MARK
for i in rw] for j in rv]
ids = [[0 for i in rw] for j in rv]
optimal = [None, 0, 0]
for i in range(lv):
for j in range(lw):
vals = [[mat[i][j] + bl[v[i]][w[j]], DIAG_MARK],
[mat[i + 1][j] - extend - gpc[i + 1][j], VGAP_MARK],
[mat[i][j + 1] - extend - gpc[i][j + 1], HGAP_MARK]]
mat[i + 1][j + 1], pnt[i + 1][j + 1] = max(vals)
gpc[i + 1][j + 1] = create * int(pnt[i + 1][j + 1] == DIAG_MARK)
if (optimal[0] is None or mat[i + 1][j + 1] > optimal[0]) and \
abs(lv - i) / float(lv) <= options.LENGTH_ERR and \
w[j] in starts:
optimal = [mat[i + 1][j + 1], i + 1, j + 1]
i, j = optimal[1], optimal[2]
seq, ids = ['', ''], 0
gapcount, length, sublen = 0, 0, 0
methods = {
VGAP_MARK:
lambda s, i, j, l, g, n:
(['-' + s[0], w[j - 1] + s[1]], i, j - 1, l + 1, g + 1, n),
DIAG_MARK:
lambda s, i, j, l, g, n:
([v[i - 1] + s[0], w[j - 1] + s[1]], i - 1, j - 1,
l + 1, g, n + (w[j - 1] == v[i - 1])),
HGAP_MARK:
lambda s, i, j, l, g, n:
([v[i - 1] + s[0], '-' + s[1]], i - 1, j, l, g + 1, n)
}
while [i, j] != [0, 0]:
length += 1
state = (seq, i, j, sublen, gapcount, ids)
seq, i, j, sublen, gapcount, ids = methods[pnt[i][j]](*state)
return {
'subject': seq[0][::-1],
'query': seq[1][::-1],
'score': optimal[0],
'gaps': gapcount,
'length': length,
'sublength': sublen,
'identities': ids
}