def weightedLoad(infile,weightthresh=None):
myAlign = simformat.read(infile)
myHeader = myAlign.header
if weightthresh is not None:
try:
weightsindex = myHeader.cutoffs.index(weightthresh)
except:
raise Exception("No such weighting cutoff, valid cutoffs are: " + repr(myHeader.cutoffs))
simformat.annotateAlignment(myAlign)
weights = S.array(simformat.getinvnormsim(myAlign,weightsindex))
else:
weights = S.ones(len(myAlign))
N = len(myAlign)
Width = len(myAlign[0])
Matrix = sp.lil_matrix((N,Q*Width)) #LiL is better to populate, csc might be even better, but we'd have to write more complex code.
for seqRec,one_weight,i in izip(myAlign,weights,count()):
seq_as_ints = intConv(seqRec.seq.tostring())
for residue,j in izip(seq_as_ints,count()):
Matrix[i,j*Q + residue] = one_weight
return Matrix.tocsc()
def main():
#parse commandline arguments
parser = OptionParser(usage="Usage: %prog [options] <inputFAA> <outputSIM>")
parser.add_option('-u','--unique',dest='unique',default=True,action='store_true')
parser.add_option('-i','--ids',dest='cutoffs',type='string',default='100,98,95,90,85,80,75,70')
parser.add_option('-f','--fids',dest='fcutoffs',type='string',default=None)
options, args = parser.parse_args()
if len(args) != 2:
parser.print_help()
sys.exit()
#read the alignment from file
with open(args[0]) as infile:
myAlignment = simformat.read(infile)
if options.unique:
myAlignment._records = uniqSeqs(myAlignment._records)
simformat.annotateAlignment(myAlignment)
if options.fcutoffs is None:
thresholds = S.array(map(float,options.cutoffs.split(',')))/100.0
else:
thresholds = S.array(map(float,options.fcutoffs.split(',')))
myAlignment.header.cutoffs = thresholds
#MORE CODE HERE!!!
AsVects = [S.array(map(ord, record.seq.tostring())) for record in myAlignment]
AllSimilarities = 1.0 - D.cdist(AsVects,AsVects,'hamming')
weights = S.zeros((len(myAlignment),len(thresholds)))
for oneThresh, col in izip(thresholds,count()):
weights[:,col] = (AllSimilarities > oneThresh).sum(1)
for i in range(0,len(myAlignment)):
myAlignment._records[i].annotations["weights"] = map(int,weights[i])
#write output file
with open(args[1],"w") as outfile:
simformat.write(outfile,myAlignment)