def getseqlist(peakfilename, size=2000):
result = []
peaklist = getpeaklist(peakfilename)
for faname in falist:
fa = fafile(fadir + "/" + faname + ".fa")
for peak in peaklist:
if not peak[0] == faname: continue
subseq = fa.getsequence(peak[1], size)
if not subseq == None: result.append(subseq)
fa.close()
return result
def extractsubseq(peakname, size=2000):
fadir = "../GeneData/FA"
peakfiledir = "../GeneData/GSE11431_RAW"
seqdir = "../GeneData/SEQ"
pseqdir = seqdir + "/" + peakname
peakfilename = peakfiledir + "/" + peakname + ".txt"
fafiles = {}
seqfiles = {}
os.mkdir(pseqdir)
peakfile = peakpoint(peakfilename)
chrname, peak = peakfile.getnext()
while not chrname == None:
if not chrname in fafiles:
filename = fadir + "/" + chrname + ".fa"
fafiles[chrname] = fafile(filename)
if not chrname in seqfiles:
seqfilename = pseqdir + "/" + chrname + ".seq"
seqfiles[chrname] = open(seqfilename, 'w')
#print "index is: ", peakfile.getindex()
#print chrname, peak
subseq = fafiles[chrname].getsequence(peak, size)
if subseq == None:
#raw_input()
pass
else:
seqfiles[chrname].write(str(peak) + '\t' + subseq + '\n')
chrname, peak = peakfile.getnext()
peakfile.close()
for fadatafile in fafiles.values():
fadatafile.close()
for seqdatafile in seqfiles.values():
seqdatafile.close()
return seqfiles.keys()