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 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
#print >>sys.stderr, headers
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, motif, filter )
yield scoremax,width,headers
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
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
