def MafMotifScorer(species, maf, motifs):
width = len(maf.components[0].text)
headers = [(c.src, c.start, c.end) for c in maf.components]
# expand block rows to full
mafBlockSpecies = [
specName.src.split('.')[0] for specName in maf.components
]
alignlist = []
for sp in species:
try:
i = mafBlockSpecies.index(sp)
alignlist.append(maf.components[i].text)
except ValueError:
alignlist.append([NaN for n in range(width)])
alignrows = pwmx.Align(alignlist, headers)
# record gap positions
filter = pwmx.score_align_gaps(alignrows)
# score motif
if isinstance(motifs, list):
scoremax = {}
for string in motifs:
scoremax[string] = pwmx.score_align_motif(alignrows, string,
filter)
else:
scoremax = pwmx.score_align_motif(alignrows, motifs, filter)
yield scoremax, width, headers
def MafMotifSelect(mafblock, pwm, motif=None, threshold=0):
if motif is not None and len(motif) != len(pwm):
raise Exception("pwm and motif must be the same length")
# generic alignment
alignlist = [c.text for c in mafblock.components]
align = pwmx.Align(alignlist)
nrows, ncols = align.dims
# required sequence length
minSeqLen = len(motif)
# record the text sizes from the alignment rows
for start in range(ncols - minSeqLen):
if align.rows[0][start] == '-':
continue
subseq = ""
pwm_score_vec = []
motif_score_vec = []
max_cols = 0
for ir in range(nrows):
expanded = align.rows[ir].count('-', start, minSeqLen)
subtext = align.rows[ir][start:minSeqLen + expanded]
max_cols = max(len(subtext), max_cols)
subseq = subtext.replace('-', '')
revseq = pwmx.reverse_complement(subseq)
# pwm score
nill, f_score = pwm.score_seq(subseq)[0]
r_score, nill = pwm.score_seq(revseq)[0]
pwm_score_vec.append(max(f_score, r_score))
# consensus score
if motif is not None:
for_score = int(pwmx.match_consensus(subseq, motif))
rev_score = int(pwmx.match_consensus(revseq, motif))
motif_score_vec.append(max(for_score, rev_score))
# check threshold
try:
assert not isnan(max(pwm_score_vec))
assert not isnan(max(motif_score_vec))
except AssertionError:
print(pwm_score_vec, motif_score_vec, file=sys.stderr)
print(len(subseq), len(pwm), file=sys.stderr)
if max(pwm_score_vec) < threshold:
continue
if max(motif_score_vec) < threshold:
continue
# chop block
col_start = start
col_end = max_cols + 1
motifmaf = mafblock.slice(col_start, col_end)
yield motifmaf, pwm_score_vec, motif_score_vec
"""
def MafBlockScorer(pwm,species,maf):
width = len(maf.components[0].text)
headers = [ (c.src,c.start,c.end) for c in maf.components]
# expand block rows to full
mafBlockSpecies = [specName.src.split('.')[0] for specName in maf.components]
alignlist = []
for sp in species:
try:
i = mafBlockSpecies.index( sp )
alignlist.append( maf.components[i].text )
except ValueError:
alignlist.append( [ NaN for n in range( width ) ] )
alignrows = pwmx.Align( alignlist )
scoremax = {}
# record gap positions
filter = pwmx.score_align_gaps( alignrows )
# score pwm models
for model in pwm.keys():
#print >>sys.stderr,"%s_%d_%d" % headers[0],width,model
scoremax[model] = pwm[model].score_align( alignrows, filter )
yield scoremax,width,headers