def get_all_orfs(seqrecord, frame):
"""
Generic ORF finder; it returns a list of all ORFs as they are
found, given codons (a list if tuples in the form (codon,
position)) from `get_codons`. This list is a list of SeqRange
objects.
Earlier versions did not allow for overlapping ORFs, since our
approach was to always take the 5'-most start codon. However, now
new versions will allow for other start codon prediction methods.
For example:
|-----M---M---M----------------*----|
Earlier methods would just give a single ORF candidate:
|----------ORF-----------|
|-----M---M---M----------------*----|
Now, this new version will allow overlapping ORFs (via a queue):
|-----ORF3-------|
|---------ORF2-------|
|-------------ORF1-------|
|-- open ended case -----------|
|-----M---M---M----------------*----|
Save for annotating them differently, this function will not
ignore partial 5'-incomplete for 3'-incomplete cases. In other
words, we assume we are in an open reading frame from the
start. This allows us to enumerate every biologically possible
ORF.
"""
seq = seqrecord.seq
seqname = seqrecord.id
seqlength = len(seq)
# initialize ORF collector, and starting positions
all_orfs = SeqRanges() # for final ORFs
# to handle keeping many reading possible reading frame candidates
# open at once, we use a queue. Tuples maintain key data:
# (start orf position, start query position, whether had start codon)
orf_queue = deque(list())
# get all codons in frame
codons = get_codons(seq, frame)
# push case that we're in reading frame from start onto queue, but
# only if it's not a stop codon
codon, orf_pos, query_pos = codons[0]
if codon not in STOP_CODONS:
# note what we're adding here: query_pos is query position *in
# frame*. So even if the ORF is open-ended, we will still not
# start from the beginning of the sequence, but rather the
# beginning of the sequence in frame.
orf_queue.append((orf_pos, query_pos, False))
for codon, orf_pos, query_pos in codons:
codon = codon.upper()
if codon in START_CODONS:
#print "adding start codon '%s' pos %d to queue" % (codon, query_pos)
orf_queue.append((orf_pos, query_pos, True))
continue
if codon in STOP_CODONS:
# pop everything off queue and make it an ORF to add to
# the candidates list
while True:
try:
orf_start_pos, query_start_pos, had_start = orf_queue.popleft()
except IndexError:
break
orf_data = {"no_start":not had_start, "no_stop":False}
orf = SeqRange(Range(query_start_pos, query_pos+2), seqname,
"+", seqlength=seqlength, data=orf_data)
all_orfs.append(orf)
# iteration complete. If there are still items in the ORF queue,
# pop them off and add them as incomplete.
if len(orf_queue) > 0:
while True:
try:
orf_start_pos, query_start_pos, had_start = orf_queue.pop()
except IndexError:
break
orf_data = {"no_start":not had_start, "no_stop":True}
orf = SeqRange(Range(query_start_pos, query_pos+2), seqname,
"+", seqlength=seqlength, data=orf_data)
all_orfs.append(orf)
return all_orfs
