from TAMO import MotifTools from TAMO.seq import Fasta from TAMO.MotifMetrics import ProbeSet from TAMO.MD.AlignAce import AlignAce from TAMO.MD.MDscan import MDscan from TAMO.MD.Meme import Meme #from TAMO.DataSources import GO from time import time fastaPath = '/Users/biggus/Documents/James/Data/ClusterDefs/TC-Fastas/TC-96.oneLine.fas' clusterIDS = Fasta.ids(fastaPath) totalSeqs = ProbeSet(fastaPath) # !! this is wrong should proly be goodAffys MDbg = '/Users/biggus/Documents/James/Data/2KB/2kb_Sequence/2kb_Anopheles/2KBupTSS_goodAffyAGAPsFastasOUT.masked.nr.MD.bg' outFile = '/Users/biggus/Documents/James/Data/ClusterDefs/testTAMOmetrics.txt' #theAce = AlignAce(fastaPath,width=10) print 'running MDscan...' tMD_1 = time() MDmotifs = MDscan(fastaPath) #,bgfile=MDbg) tMD_2 = time() MD_time = tMD_2-tMD_1 print 'MDscan took %.5f sec == %.3f min.\nMDscan found %s motifs.' % (MD_time,MD_time/60.0, len(MDmotifs.motifs)) print 'running MEME...' tMeme_1 = time() memeMotifs = Meme(fastaPath) tMeme_2 = time() Meme_time = tMeme_2-tMeme_1
from TAMO import MotifTools from TAMO.seq import Fasta from TAMO import MotifMetrics from TAMO.MD.AlignAce import AlignAce from TAMO.MD.MDscan import MDscan from TAMO.MD.Meme import Meme from TAMO import Clustering #from TAMO.DataSources import GO from time import time TC8_path = '/Users/biggus/Documents/James/Data/ClusterDefs/TC-Fastas/TC-8.fas' TC8_ids = Fasta.ids(TC8_path) TC8_seqs = Fasta.seqs(TC8_path) allSeqs = MotifMetrics.ProbeSet('/Users/biggus/Documents/James/Data/2KB/2kb_Sequence/2kb_Anopheles/2KBupTSS_goodAffyAGAPsFastasOUT.masked.nr.fas') outFile = '/Users/biggus/Documents/James/Data/ClusterDefs/TC-8_MotifMetrics.5-12.txt' roughBestKmers = [] for i in range(6,10): imers = MotifMetrics.top_nmers_seqs(i,TC8_seqs) roughBestKmers.extend(imers) print '%s %smers found.' % (len(imers), i) kmerMetrics = ['Kmer\thGeoPval\tBinomOverRep\n'] for kmer in roughBestKmers: hGeoPval = allSeqs.Enrichment(kmer, TC8_ids) binom = allSeqs.overrep(kmer,TC8_ids) kmerMetrics.append('%s\t%s\t%s\n' % (kmer,hGeoPval,binom))