'/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()