'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/MemeResults/Clus2_247gene_0.8_Apr16_14-46-33.meme.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/AceResults/Clus2_247gene_0.8_Apr16_14-46-36.ace.3.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/AceResults/Clus2_247gene_0.8_Apr16_14-46-36.ace.1.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/AceResults/Clus2_247gene_0.8_Apr16_14-46-33.ace.3.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/AceResults/Clus2_247gene_0.8_Apr16_14-46-33.ace.2.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/RandSplitFastas/AceResults/Clus2_247gene_0.8_Apr16_14-46-33.ace.1.txt.tmo',
'/Users/biggus/Documents/James/Data/ReClustering/PrelimData_Grant_Feb09/Clus2_247genes.6-8mers.gGEMS.tmo']
motifs = []
if tPkls != None:
for p in tPkls:
motifs.extend(cPickle.load(open(p, 'r')))
if tmoFiles != None:
for t in tmoFiles:
motifs.extend(loadTMOs(t))
motifs = convertTAMOs2MOPATs(motifs)
# print to file
keys = sorted(motifs.keys(),key=lambda x: int(x.split('_')[0]))
outFile = open(outFile, 'w')
for k in keys:
toOut = '>%s\tBlank\n' % (k)
for i in range(len(motifs[k])):
toOut += '%s\n' % (' '.join(map(lambda x: str(x),motifs[k][i])))
outFile.write(toOut)
outFile.close()
if tPkls: lenFiles += len(tPkls)
if tmoFiles: lenFiles += len(tmoFiles)
motifs = []
if tPkls != None:
for p in tPkls:
Ms = cPickle.load(open(p, 'r'))
for i in range(len(Ms)):
Ms[i].sourceFile = p
motifs.extend(Ms)
print '%s motifs from %s' % (len(Ms), p.split('/')[-1])
if tmoFiles != None:
for t in tmoFiles:
Ms = loadTMOs(t)
for i in range(len(Ms)):
Ms[i].sourceFile = t
motifs.extend(Ms)
print '%s motifs from %s' % (len(Ms), t.split('/')[-1])
motifDict = {}
mCount = 0
for m in motifs:
mCount+=1
motifDict['%03d_%s' % (mCount, m.oneletter)] = m
print '%s motifs loaded from %s files.' % (len(motifs), lenFiles)
t1 = time()
maps = MapLib(fastaPath,motifDict, thresh=0.7)
t2 = time()
