def orf_finder(sequence,startphase,stopphase,strand,expected_aa_len,length_variance,
search_coords = None, is_start = False, is_stop = False, hmm_profile = None,evalue='0.05'):
"""Finds all putative exons matching a given expected length and intron phase profile and \
containing an open reading frame"""
search_seq = sequence
if search_coords:
search_seq = sequence[search_coords[0]:search_coords[1]]
if strand == '+':
search_seq = genome.Sequence(search_seq)
elif strand == '-':
search_seq = genome.Sequence(search_seq).reverse_compliment()
match_len = expected_aa_len * 3 + ((3 - startphase) % 3) + stopphase
phase_matches = []
startstop = ['AG','G[TC]']
if is_start:
startstop[0] = 'ATG'
match_len = match_len - 3
if is_stop:
startstop[1] = "T(AG|GA|AA)"
match_len = match_len - 3
for variance in range(length_variance + 1):
for direction in (1,-1):
if variance == 0 and direction == -1: # prevents double returns of 0 variance
continue
for match in re.finditer(startstop[0] + '.{' + str(match_len + variance * 3 * direction) +
'}' + startstop[1], search_seq):
phase_matches.append([match.start(), match.start() + match_len + variance * 3 *
direction + len(startstop[0]) + len(startstop[1])])
exon_coords = []
for match_coords in phase_matches:
start = match_coords[0] + len(startstop[0])
stop = match_coords[1] - len(startstop[1])
if stop - (start + ((3 - startphase) % 3)) > 2:
if not "*" in genome.Sequence(search_seq[start + ((3 - startphase) % 3) : stop ]).translate():
#NB: returns 1-based coords consistent with gff and blast coords
exon_coords.append([start + 1,stop])
if is_start:
exon_coords[-1][0] = exon_coords[-1][0] - 3
if is_stop:
exon_coords[-1][1] = exon_coords[-1][1] + 3
if strand == '-':
exon_coords[-1] = [len(search_seq) - exon_coords[-1][1] + 1,len(search_seq) - exon_coords[-1][0] + 1]
if search_coords:
exon_coords[-1] = [exon_coords[-1][0] + search_coords[0],exon_coords[-1][1] + search_coords[0]]
if hmm_profile and len(exon_coords) > 0:
exon_coords = hmmsearch(hmm_profile,exon_coords,sequence,strand,startphase,evalue=evalue)
return exon_coords
def hmmsearch(hmm_profile,exon_coords,sequence,strand,startphase, evalue= "0.05"):
orf_file = tempfile.NamedTemporaryFile('w')
for coords_index in range(len(exon_coords)):
nuc_seq = genome.Sequence(sequence[exon_coords[coords_index][0] - 1:exon_coords[coords_index][1]])
if strand == '-':
nuc_seq = nuc_seq.reverse_compliment()
pep_seq = genome.Sequence(nuc_seq[((3 - startphase) % 3):]).translate()
orf_file.write(">coords" + str(coords_index) + '\n' +
pep_seq + '\n' )
orf_file.flush()
hmmout = subprocess.check_output('hmmsearch --max -E ' + evalue + ' ' + hmm_profile + ' ' + orf_file.name,
shell = True).split('\n')
found_hit = False
for line in hmmout:
if line[:2] == ">>":
found_hit = True
return exon_coords[int(line[9:].replace('\r',''))]
break
if not found_hit:
return []
#sets up default program paths, overwritten by any program paths passes with -f or --program_filepaths
hmmsearch = args.hmmsearch_filepath
target_nucdb = genome.Genome(args.target_nucdb)
#Gets ORFs from the genome and hmmers them
if args.frames_in:
frames_file = args.frames_in
else:
if args.frames_out:
frame_fasta = open(args.frames_out, 'w')
else:
frame_fasta = tempfile.NamedTemporaryFile('w')
for seq_id in target_nucdb.genome_sequence:
frameonef = genome.Sequence(target_nucdb.genome_sequence[seq_id])
frameoner = genome.Sequence(
target_nucdb.genome_sequence[seq_id]).reverse_compliment()
frames = [
frameonef,
genome.Sequence(frameonef[1:]),
genome.Sequence(frameonef[2:]), frameoner,
genome.Sequence(frameoner[1:]),
genome.Sequence(frameoner[2:])
]
fasta_list = []
for frame_num in (0, 1, 2, 3, 4, 5):
frame = frames[frame_num]
if frame_num < 3:
frame_offset = frame_num
else:
def exon_finder(tstart,tend,strand,qstart,qend,qlen,qstartphase,qendphase,seqdict,seqname,
max_offset = 30, is_start = False, is_stop = False, nevermind_atg = False):
""""finds exons with ORFs based on the requested parameters. Note that it is expected that tstart < tend, \
even for minus strand features, so these might need to be reversed if coming from say tblastn. \
Also coords are expected as 1-based (as output from blast), and are \
converted internally to 0 based. It is also expected that the hit itself doesn't contain stop codons."""
start = None
end = None
pseudo = False
if strand == "+":
phasestart_offset = (3 - qstartphase) % 3
phasestop_offset = qendphase
start_match_offset, stop_match_offset = 3 * (qstart - 1),3 * (qlen - qend)
elif strand == '-':
phasestart_offset = qendphase
phasestop_offset = (3 - qstartphase) % 3
start_match_offset, stop_match_offset = 3 * (qlen - qend), 3 * qstart
ideal_start = tstart - phasestart_offset - start_match_offset
ideal_end = tend + stop_match_offset + phasestop_offset
pseudo_start = tstart - phasestart_offset
pseudo_end = tend + phasestop_offset
gc_start, gc_end = None, None
for offset in range(0,max_offset + 3,3):
if start:
break
for direction in [1,-1]:
test_start = ideal_start - offset * direction
test_seq = genome.Sequence(seqdict[seqname][test_start-1 + phasestart_offset:tend])
if strand == "-":
test_seq = test_seq.reverse_compliment()
if not test_seq.translate():
continue
elif is_stop and strand == "-":
if ideal_start - 1 < test_start < pseudo_start:
pseudo_start = test_start
lastcodon = seqdict[seqname][test_start - 1:test_start + 2]
if lastcodon.upper() in ['TTA','TCA','CTA'] and test_seq.translate().count('*') == 1:
start = test_start
break
elif not "*" in test_seq.translate():
if ideal_start - 1 < test_start < pseudo_start:
pseudo_start = test_start
if is_start and strand == '+':
if nevermind_atg:
start = test_start
break
else:
firstcodon = seqdict[seqname][test_start - 1:test_start + 2]
if firstcodon.upper() == "ATG":
start = test_start
break
else:
splicesite = seqdict[seqname][test_start-3:test_start-1]
if (strand == '+' and splicesite.upper() == "AG") or (strand == '-' and splicesite.upper() == "AC"):
start = test_start
break
elif strand == '-' and splicesite.upper() == "GC" and not gc_start:
gc_start = test_start
if not start:
if gc_start:
start = gc_start
else:
pseudo = "P"
start = pseudo_start
for offset in range(0,max_offset + 3,3):
if end:
break
for direction in [-1,1]:
test_end = ideal_end - offset * direction
if test_end - start < 3:
break
test_seq = genome.Sequence(seqdict[seqname][start - 1 + phasestart_offset:test_end - phasestop_offset])
if strand == "-":
test_seq = test_seq.reverse_compliment()
if not test_seq.translate():
continue
elif is_stop and strand == "+":
if ideal_end + 1 > test_end > pseudo_end:
pseudo_end = test_end
lastcodon = seqdict[seqname][test_end - 3:test_end]
if lastcodon.upper() in ['TAA','TGA','TAG'] and test_seq.translate().count('*') == 1:
end = test_end
break
elif not "*" in test_seq.translate() or (is_stop and not "*" in test_seq.translate()[:-1]):
if ideal_end + 1 > test_end > pseudo_end:
pseudo_end = test_end
if is_start and strand == '-':
if nevermind_atg:
end = test_end
break
else:
firstcodon = seqdict[seqname][test_end - 3:test_end]
if firstcodon.upper() == "CAT":
end = test_end
break
else:
splicesite = seqdict[seqname][test_end:test_end + 2]
if (strand == '+' and splicesite.upper() == "GT") or (strand == '-' and splicesite.upper() == "CT"):
end = test_end
break
elif strand == "+" and splicesite.upper() == "GC" and not gc_end:
gc_end = test_end
if not end:
if gc_end:
end = gc_end
else:
pseudo = "P"
end = pseudo_end
return [start,end,pseudo]