def stitch(record1, record2):
seq1 = array([record1.seq.tostring()])
seq2 = array([reverse_complement(record2.seq.tostring())])
seq1.dtype = '|S1'
seq2.dtype = '|S1'
quals1 = array(record1.letter_annotations['phred_quality'])
quals2 = array(record2.letter_annotations['phred_quality'][::-1])
log10p_consensus_1 = log1p(-power(10, -quals1 / 10.)) / log(10)
log10p_consensus_2 = log1p(-power(10, -quals2 / 10.)) / log(10)
log10p_error_1 = -log10(3) - (quals1 / 10.)
log10p_error_2 = -log10(3) - (quals2 / 10.)
min_overlap = 1
max_overlap = max(len(record1), len(record2))
overlaps = {}
for overlap in range(1, max_overlap):
s1 = seq1[-overlap:]
s2 = seq2[:overlap]
q1 = quals1[-overlap:]
q2 = quals2[:overlap]
lpc1 = log10p_consensus_1[-overlap:]
lpc2 = log10p_consensus_2[:overlap]
lpe1 = log10p_error_1[-overlap:]
lpe2 = log10p_error_2[:overlap]
consensus = choose(q1 < q2, [s1, s2])
score = sum(choose(consensus == s1, [lpe1, lpc1])) + sum(choose(consensus == s2, [lpe2, lpc2])) + len(consensus) * log10(4) * 2 # last term is null hypothesis, p=1/4
consensus.dtype = '|S%i' % len(consensus)
overlaps[overlap] = (consensus[0],score)
return overlaps
def build_aln(alnsummary, vulgar_commands, queryseq, targetseq):
"""Build full alignment from exonerate using 'parsable' preset and vulgar output"""
queryname = alnsummary['query_id']
targetname = alnsummary['target_id']
# process strands. the position vars below will always progress
# from 0->len(seq), so the seqs must be revcomped accordingly
queryposition = alnsummary['query_aln_begin']
targetposition = alnsummary['target_aln_begin']
if alnsummary['query_strand'] == '-':
queryseq = seqtools.reverse_complement(queryseq)
queryposition = len(queryseq) - queryposition
if alnsummary['target_strand'] == '-':
targetseq = seqtools.reverse_complement(targetseq)
targetposition = len(targetseq) - targetposition
pad = abs(queryposition - targetposition)
# build alignment
queryaln = ''
targetaln = ''
# process necessary padding
if queryposition > targetposition:
targetaln = ' ' * pad
else:
queryaln = ' ' * pad
# add pre-aln sequence
queryaln += queryseq[0:queryposition]
targetaln += targetseq[0:targetposition]
# walk through alignment (from vulgar output)
for cmd in vulgar_commands:
if cmd[0] == 'M':
assert (cmd[1] == cmd[2])
queryaln += queryseq[queryposition:queryposition + cmd[1]]
targetaln += targetseq[targetposition:targetposition + cmd[2]]
queryposition += cmd[1]
targetposition += cmd[2]
elif cmd[0] == 'G':
assert ((cmd[1] == 0) != (cmd[1] == 0)) # xor
if cmd[1] == 0:
queryaddendum = '-' * cmd[2]
targetaddendum = targetseq[targetposition:targetposition +
cmd[2]]
elif cmd[2] == 0:
queryaddendum = queryseq[queryposition:queryposition + cmd[1]]
targetaddendum = '-' * cmd[1]
queryaln += queryaddendum
targetaln += targetaddendum
queryposition += cmd[1]
targetposition += cmd[2]
else:
raise ValueError, "I do not understand the vulgar command %s" % cmd[
0]
# add any post-aln sequence
queryaln += queryseq[queryposition:]
targetaln += targetseq[targetposition:]
return (queryaln, targetaln)
def seqdict2revcompseqdict(seqdict):
revcompdict = {}
for item in seqdict.iteritems():
revcompdict[item[0]] = seqtools.reverse_complement(item[1])
return revcompdict
def seqdict2revcompseqdict(seqdict):
revcompdict = {}
for item in seqdict.iteritems():
revcompdict[item[0]] = seqtools.reverse_complement(item[1])
return revcompdict
def build_aln(alnsummary,vulgar_commands,queryseq,targetseq):
"""Build full alignment from exonerate using 'parsable' preset and vulgar output"""
queryname = alnsummary['query_id']
targetname = alnsummary['target_id']
# process strands. the position vars below will always progress
# from 0->len(seq), so the seqs must be revcomped accordingly
queryposition = alnsummary['query_aln_begin']
targetposition = alnsummary['target_aln_begin']
if alnsummary['query_strand'] == '-':
queryseq = seqtools.reverse_complement(queryseq)
queryposition = len(queryseq) - queryposition
if alnsummary['target_strand'] == '-':
targetseq = seqtools.reverse_complement(targetseq)
targetposition = len(targetseq) - targetposition
pad = abs(queryposition - targetposition)
# build alignment
queryaln = ''
targetaln = ''
# process necessary padding
if queryposition > targetposition:
targetaln = ' ' * pad
else:
queryaln = ' ' * pad
# add pre-aln sequence
queryaln += queryseq[0:queryposition]
targetaln += targetseq[0:targetposition]
# walk through alignment (from vulgar output)
for cmd in vulgar_commands:
if cmd[0] == 'M':
assert(cmd[1]==cmd[2])
queryaln += queryseq[queryposition:queryposition+cmd[1]]
targetaln += targetseq[targetposition:targetposition+cmd[2]]
queryposition += cmd[1]
targetposition += cmd[2]
elif cmd[0] == 'G':
assert( (cmd[1]==0) != (cmd[1]==0) ) # xor
if cmd[1] == 0:
queryaddendum = '-' * cmd[2]
targetaddendum = targetseq[targetposition:targetposition+cmd[2]]
elif cmd[2] == 0:
queryaddendum = queryseq[queryposition:queryposition+cmd[1]]
targetaddendum = '-' * cmd[1]
queryaln += queryaddendum
targetaln += targetaddendum
queryposition += cmd[1]
targetposition += cmd[2]
else:
raise ValueError, "I do not understand the vulgar command %s" % cmd[0]
# add any post-aln sequence
queryaln += queryseq[queryposition:]
targetaln += targetseq[targetposition:]
return (queryaln,targetaln)