def calPvalues(siRNASeeds,seedfile,outfile,method='RRA',N=10000):
# read headers
print >>sys.stderr, Utils.touchtime(),"reading header"
fh = gzip.open(seedfile,'rb')
genes,lengths = SeedUtils.parseHeader(fh)
num_genes = len(genes)
# aRRA
print >>sys.stderr, Utils.touchtime(),"start analyzing data."
method = {'RRA':SeedUtils.aRRA}.get(method,SeedUtils.aRRA)
escores = numpy.zeros(num_genes)
for i in range(0,num_genes,N):
n = N if i+N < num_genes else num_genes%N
if n:
geneSeeds = numpy.sum(numpy.frombuffer(fh.read(2**17*n),dtype=numpy.uint16,count=2**16*n).reshape((n,4,2**14)),axis=1)
escores[i:i+n] = method(siRNASeeds,geneSeeds)
print Utils.touchtime(), "analyzed", i+n
fh.close()
# Writting result to file
print >>sys.stderr, Utils.touchtime(), 'writing result to file.'
df = pandas.DataFrame({'gid':genes,'length':lengths, 'escore':escores})
rv = SeedUtils.evdplot(df,outfile+".pdf")
df.loc[:,'pvalue'] = rv.pdf(df.escore)
df = df.sort_values(by='pvalue',ascending=False)
df.to_csv(outfile,index=False,sep='\t',columns=['gid','length','escore','pvalue'])
print >>sys.stderr, Utils.touchtime(), "finished."
return df
def parseGeneSeeds(gfile,dumpfile,N=10):
'''
Parse seeds on gene sequences.
Parameters:
gfile: string
Gene sequence file in Fasta format.
N: int
Parse N sequence at a time instead all to reduce memory usage. [Default=10000]
N = 10000, memory usage for the two huge matrix is up to 1.83G.
'''
# create seed tables
SeedUtils.createTables()
# read genes
ofh = gzip.open(dumpfile,'wb')
genes = [fa for fa in IO.BioReader(gfile,'fasta')]
# write headers
gids = ';'.join(["{0}:{1}".format(fa.id,len(fa)) for fa in genes])
header = numpy.array([0x19840405,len(genes),len(gids)],dtype=numpy.uint64)
ofh.write(header.data)
ofh.write(gids)
# parse genes
cnt = 0
mat = numpy.zeros((N,2**15),dtype=numpy.uint16)
seeds = numpy.zeros((N,4,2**14),dtype=numpy.uint16) # N x type x seeds
for fa in genes:
SeedUtils.findSeeds(fa.seq.seq.upper(),mat[cnt%N])
cnt += 1
if cnt%(N)==0:
# calculate seeds for the N genes
SeedUtils.parseSeeds(mat,seeds)
ofh.write(seeds.data)
print >>sys.stderr, touchtime(), "Parsed {0} genes .".format(cnt)
seeds.fill(0)
mat.fill(0)
# calculate seeds for the rest of genes
rest = cnt%N
if rest:
SeedUtils.parseSeeds(mat[:rest],seeds[:rest])
ofh.write(seeds[:rest].data)
print >>sys.stderr, Utils.touchtime(), "Parsed {0} genes. ".format(cnt)
ofh.close()
