def full_transposon_treatment(seq,overlap,gap,minlength,fastaout,evalue=None,
fname=None):
'''This is where it all comes together. This takes a sequence of
hits, assumed to constitute an entire a blast search between one
transposon and one fly genome. (See note below.) It performs the
main process of this module -- i.e., creating the input for a
multiple-alignment -- and dumps that information in FASTA format
to *fastaout*, which must be a writeable fasta object (see module
*fasta*). The user is naturally responsible for closing both, if
appropriate (as it is in almost all cases).
NOTE: Generally it is best to have *seq* come from the function
hitsfromcsv(). This can be done implicitly by giving None as the
first argument, in which case *f* is expected to be a file object
or filename to be given to hitstocsv().
'''
if None not in (seq,fname):
raise Error("Cannot give both seq and fname arguments")
elif seq is None: seq = hitsfromcsv(fname)
for s,hits in utils.groupby(seq,key=_attrget('SSEQID')).iteritems():
for island in makeislands(hits,gap):
singles,nests = classifyrecords(island,overlap)
nests = [stratify(N,minlength) for N in nests]
if singles or any(nests):
fastaout.writeentries(resolve_query_overlap(singles,nests,overlap))
else: raise Error('No records result from file {!r}'.format(fname))
def stratify(nest,minlength):
'''Generator function that takes a nest, i.e. a list of hits for which
each adjacent pair has nontrivial overlap in the subject ordinates,
and yields according to the following process:
- Yield x, the hit with lowest EVALUE (largest length is tiebreaker)
- For each other hit y, truncate (or if necessary, split) y so as to
remove any overlap with x. If this makes y a trivial hit, i.e. one
whose length is less than minlength, remove it from the nest entirely.
- Repeat until the nest has been exhausted.
The process is actually implemented in an abstract fashion using a
helper function - see _stratify().
'''
return _stratify(nest,
rank=hit_rank,
filterfunc=lambda x: x.LENGTH > minlength,
sget=_attrget('_SSTART'),
eget=_attrget('_SEND'),
sset=set__SSTART,
eset=set__SEND)
def resolve_query_overlap(standalones,nests,overlap):
'''Expects a list of standalone fragments and a list of nests. Nests are
expected to have undergone the subject overlap truncation scheme (see
*stratify*). The return value is a list of fasta entries. If the function
detects no query overlap between any pair of fragments -- including those
in nests -- the fragments are "assembled" (non-technical term) in order
of query-ordinates into a single fasta entry, which is the only element of
the returned list.
'''
standalones = list(standalones)
nests = map(list,nests)
if not (standalones or any(nests)):
raise Error('Tried to resolve query overlap on an empty set of records!')
# assign names before reordering
for j,hit in enumerate(standalones): setname(hit,'standalone[{}]'.format(j))
for i,nest in enumerate(nests,1):
for j,hit in enumerate(nest): setname(hit,'nest{}[{}]'.format(i,j))
# and then reorder by query ordinate
recs = sorted(_it.chain(standalones,*nests),key=_attrget('QSTART'))
if any(q_overlap(x,y)>=overlap for x,y in _it.izip(recs,recs[1:]))\
or len(recs)==1: return _it.imap(make_entry,recs)
prev = None
with _cont.closing(_sIO()) as seq:
for hit in recs:
seq.write('-'*(hit.QSTART-1-( prev and prev.QEND or 0 )))
if prev is None: st,end = hit._SSTART,hit._SEND
else: st,end = min(st,hit._SSTART),max(end,hit._SEND);
seq.write(hit.SSEQ)
prev = hit
result = fasta.seq_entry({'SEQ': seq.getvalue(),
'NAME': _name_fmt.format(_GRP='all',SSEQID=recs[0].SSEQID,
SSTART=min(h._SSTART for h in recs),SEND=max(h._SEND for h in recs))})
return [result]
def s_overlap(x,y):
'''Returns the number of base pairs by which the subject ordinates of x
and y overlap. Returns zero if and only if they are disjoint.'''
return _overlap(x,y,_attrget('_SSTART'),_attrget('_SEND'))
def q_overlap(x,y):
'''Returns the number of base pairs by which the query ordinates of x
and y overlap. Returns zero if and only if they are disjoint.'''
return _overlap(x,y,_attrget('QSTART'),_attrget('QEND'))
def s_distance(x,y):
'''Measures distance between the query ordinates of x and y. Returns 1
if they are adjacent, 0 if they overlap.'''
return _dist(x,y,_attrget('QSTART'),_attrget('QEND'))