def getSeqFreqs(seqDict):
""""Returns tuple with correct values for motility
AT_bias,GC_bias keywords as calculated from seqDict."""
# These look weird bc motility expects these info in a weird way.
# I have confirmed from Titus Brown (motility author) that this is correct.
GC_bias = seqStats(seqDict)['percentGC']/2
AT_bias = 0.5 - GC_bias
return AT_bias,GC_bias
def getSeqFreqs(seqDict):
""""Returns DICT with correct values for TAMO
AT_bias,GC_bias keywords as calculated from seqDict."""
data = seqStats(seqDict)
seqFreqs = {}
seqFreqs['A'] = float(data['aCnt'])/data['nonNs']
seqFreqs['C'] = float(data['cCnt'])/data['nonNs']
seqFreqs['G'] = float(data['gCnt'])/data['nonNs']
seqFreqs['T'] = float(data['tCnt'])/data['nonNs']
return seqFreqs
def toTAMOmotifs(motifList,seqData=None):
"""Returns a list of TAMO motif Objects when given
a list of the native motif Objs.
If seqData is a dict, it is assumed to be
nucFreqs (seqData['A']==.26),
else, it is assumed to be a path to a seqPopulation
that the motifs will be used on for stats to be
calculated against."""
from TAMO.MotifTools import Motif_from_counts
if not seqData:
if type(seqData) == type({}):
try:
aFreq = seqData['A']
cFreq = seqData['C']
gFreq = seqData['G']
tFreq = seqData['T']
except KeyError:
raise InvalidOptionError("toTAMOmotifs: Unrecognized key in seqData as dict.")
elif type(seqData) == type(''):
sDict = ParseFastA(seqData).toDict()
seqData = seqStats(sDict)
del(sDict)
tot = float(seqData['nonNs'])
aFreq = seqData['aCnt']/tot
cFreq = seqData['cCnt']/tot
gFreq = seqData['gCnt']/tot
tFreq = seqData['tCnt']/tot
else:
aFreq = 0.25
cFreq = 0.25
gFreq = 0.25
tFreq = 0.25
tList = []
for m in motifList:
counts = []
for i in range(len(m)):
counts.append({'A':m.pwm['A'][i],'C':m.pwm['C'][i],'G':m.pwm['G'][i],'T':m.pwm['T'][i]})
t = Motif_from_counts(counts,beta=0.01,bg={'A':aFreq,'C':cFreq,'G':gFreq,'T':tFreq})
t.id = m.id
try:
t.sigvalue = m.sigvalue
except AttributeError:
pass
tList.append(t)
return tList
def main():
#+++++++++++ File Parseing Etc +++++++++++
desc = """Calls the folowing funcs: 'add this'"""
usage = """python %prog args"""
parser = optparse.OptionParser(usage=usage, description=desc)
parser.add_option('--motifs', type='str',default=None,
help="""Path to motif file (default=%default).""")
parser.add_option('--motif-type', type='str',default='scope',
help="""Format of motif file (default=%default).""")
parser.add_option('--thresh', type='float',default=0.005,
help="""P-value threshold for motif score cut-off (default=%default).""")
parser.add_option('--promoters', type='str',default=None,
help="""Path to fasta file with promoter population (default=%default).""")
parser.add_option('--plen', type='int',default=1000,
help="""Max promoter length to use -- starting from 3'-end!! (default=%default).""")
parser.add_option('--genes', type='string',default=None,
help="""Unbroken string of gene/Tx names representing the true forground set, sep=','. Exp: 'gene,gene,gene' (default=%default).""")
parser.add_option('--job', type='string',default='int(time())',
help="""String to identify this run (default=%default).""")
parser.add_option('--out', type='string',default=None,
help="""Path to results dir -- must use full path (default=%default).""")
parser.add_option('--plot-fdrs', dest="fdrs", type='int',default=0,
help="""How many random sets of genes equal in length to --genes to run for FDR estimation. (default=%default).""")
parser.add_option('--from-possum',default=False,
help="""Path to possumSearch outFile, skips motif finding step. (default=%default)""")
parser.add_option('--verbose',action='store_true',default=False,
help="""Include if stdOut/stdErr is desired. (default=%default).""")
parser.add_option('--check-seqs',action='store_true',default=False,
help="""Print info about promoter sequences and exit. (default=%default).""")
parser.add_option('--expect',action='store_true',default=False,
help="""Use median seqLen to set success threshold at greater than the estimated expected number of occurences in each promoter [pValThresh*searchesPerSeq]. (default=%default).""")
(opts, args) = parser.parse_args()
# +++++ Argument Validations +++++
if len(sys.argv) == 1:
parser.print_help()
exit(0)
if not opts.out:
raise InvalidOptionError("--out argument is required.")
if not opts.genes:
raise InvalidOptionError('--genes argument is required.')
if opts.job == 'int(time())':
opts.job = int(time())
if not opts.from_possum:
if not opts.motifs or opts.motif_type or opts.thresh or opts.promoters or opts.plen:
raise InvalidOptionError("""Unless --from-possum, the following argument are ALL required:
--motif-type
--thresh
--plen""")
else:
if not opts.motifs:
raise InvalidOptionError("When using --from-possum, --motifs should be the PSSM file used to generate this particular hit set.")
# +++++ Lets Begin +++++
if opts.verbose: sys.stdout.write('\n%s\n\n' % (' '.join(sys.argv)))
if opts.verbose: sys.stdout.write('preparing out directory...\n')
outBaseStr = getOutBaseStr(opts.out,opts.job)
mkdirp(opts.out)
if opts.verbose: sys.stdout.write('building seqDict...\n')
seqDict = getSeqs(opts.promoters,opts.plen)
if opts.check_seqs:
seqStats(seqDict,show=True)
exit(0)
else:
seqData = seqStats(seqDict,show=False)
if opts.expect:
opts.expect = seqData['medLen']*opts.thresh*2
else:
opts.expect = 0
# --- am i doing the searching myself? ---
if not opts.from_possum:
# -- yes --
if opts.verbose: sys.stdout.write('building motifList...\n')
motifList = getMotifs(opts.motifs,opts.motif_type)
if opts.verbose: sys.stdout.write('getting nucFreqs...\n')
halfAT,halfGC = getSeqFreqs(seqDict)
if opts.verbose: sys.stdout.write('building hitDict...\n')
motifHits = getEvalHitDict(motifList,seqDict,pThresh=opts.thresh,halfAT=halfAT,halfGC=halfGC)
else:
# -- Oh thank god, no! All I have to do is some parseing! --
if opts.verbose: sys.stdout.write('skipping to building hitDict step...\n')
pACs = getPossumProfileACs(opts.motifs)
possumTable = getPossumHitTable(opts.from_possum,headers=possumHeaders)
motifHits = getPossumHitDict(possumTable,seqDict.keys(),pACs)
motifList = makeMotifListFromPossum(pACs) # create list of DummyPlug MotifObjs for compatibility
if opts.verbose: sys.stdout.write('getting forgroundSeqs...\n')
foregroundSeqs = getForeground(opts.genes)
outData = {}
if opts.verbose: sys.stdout.write('calculating real data p-values...\n')
realData = motifHyprGeoEnrichment(motifList,motifHits,foregroundSeqs,opts.expect)
appendData(realData,outData)
for i in range(opts.fdrs):
if opts.verbose: sys.stdout.write('ctrl_%s:\n' % (i))
if opts.verbose: sys.stdout.write('\tgetting random forground...\n')
rForground = getRandomForground(foregroundSeqs,seqDict)
if opts.verbose: sys.stdout.write('\tcalculating p-values...\n')
ctrlData = motifHyprGeoEnrichment(motifList,motifHits,rForground,opts.expect)
appendData(ctrlData,outData)
if opts.verbose: sys.stdout.write('writting outData...\n')
writeDataTable(outBaseStr,outData,motifList)
if opts.verbose: sys.stdout.write('plotting histograms...\n')
for m in motifList:
plotHist(outBaseStr,outData,m.id)
def main():
#+++++++++++ File Parseing Etc +++++++++++
desc = """Calls the folowing funcs: 'add this'"""
usage = """python %prog args"""
parser = optparse.OptionParser(usage=usage, description=desc)
parser.add_option('--motifs', type='str',default=None,
help="""Path to motif file (default=%default).""")
parser.add_option('--motif-type', type='str',default='scope',
help="""Format of motif file (default=%default).""")
parser.add_option('--motif-filter', type='str',default='lambda x: x',
help="""Filter fuction to allow filtering of motifs in motif file. Its a lambda function. The default returns all motifs. If you don't understand this, please leave it alone. (default=%default).""")
parser.add_option('--thresh', type='float',default=0.75,
help="""Fractional score threshold for motif score cut-off (default=%default).""")
parser.add_option('--promoters', type='str',default=None,
help="""Path to fasta file with promoter population (default=%default).""")
parser.add_option('--plen', type='int',default=None,
help="""Max promoter length to use -- starting from 3'-end!! (default=%default).""")
parser.add_option('--genes', type='string',default=None,
help="""Unbroken string of gene/Tx names representing the true forground set, sep=','. Exp: 'gene,gene,gene' (default=%default).""")
parser.add_option('--job', type='string',default='int(time())',
help="""String to identify this run (default=%default).""")
parser.add_option('--out', type='string',default=None,
help="""Path to results dir -- must use full path (default=%default).""")
parser.add_option('--plot-fdrs', dest="fdrs", type='int',default=0,
help="""How many random sets of genes equal in length to --genes to run for FDR estimation. (default=%default).""")
##parser.add_option('--from-possum',default=False,
##help="""Path to possumSearch outFile, skips motif finding step. (default=%default)""")
parser.add_option('--verbose',action='store_true',default=False,
help="""Include if stdOut/stdErr is desired. (default=%default).""")
parser.add_option('--check-seqs',action='store_true',default=False,
help="""Print info about promoter sequences and exit. (default=%default).""")
##parser.add_option('--expect',action='store_true',default=False,
##help="""Use median seqLen to set success threshold at greater than the estimated expected number of occurences in each promoter [pValThresh*searchesPerSeq]. (default=%default).""")
(opts, args) = parser.parse_args()
# +++++ Argument Validations +++++
if len(sys.argv) == 1:
parser.print_help()
exit(0)
if not opts.out:
raise InvalidOptionError("--out argument is required.")
if not opts.genes:
raise InvalidOptionError('--genes argument is required.')
if opts.job == 'int(time())':
opts.job = int(time())
if not (opts.motifs or opts.motif_type or opts.thresh or opts.promoters):
raise InvalidOptionError("""Unless --from-possum, the following argument are ALL required:
--motif-type
--thresh""")
if not opts.motif_filter.startswith('lambda x:'):
raise InvalidOptionError("**ERROR: the --motif-function option must begin with 'lambda x:'**")
else:
opts.motif_filter = eval(opts.motif_filter)
if opts.plen:
try:
opts.plen = int(opts.plen)
except ValueError:
raise InvalidOptionError("**ERROR: the --plen option must be a number**")
# +++++ Lets Begin +++++
if opts.verbose: sys.stdout.write('\n%s\n\n' % (' '.join(sys.argv)))
if opts.verbose: sys.stdout.write('preparing out directory...\n')
outBaseStr = getOutBaseStr(opts.out,opts.job)
mkdirp(opts.out)
if opts.verbose: sys.stdout.write('building seqDict...\n')
probeset = getProbSet(opts.promoters,opts.thresh)
#print len(probeset.probes.items()[0][1])
#print probeset.probes.items()[0][1]
if opts.plen:
if opts.verbose: sys.stdout.write("adjusting promoter lengths to no more than %s and conserving the 3' ends...\n" % (opts.plen))
for s in probeset.probes.iteritems():
probeset.probes[s[0]]= s[1][-opts.plen:]
#print len(probeset.probes.items()[0][1])
#print probeset.probes.items()[0][1]
seqDict = getSeqs(probeset)
if opts.check_seqs:
seqStats(seqDict,show=True)
exit(0)
if opts.verbose: sys.stdout.write('getting nucFreqs...\n')
nucFreqs = getSeqFreqs(seqDict)
if opts.verbose: sys.stdout.write('building filtered motifList...\n')
motifList = getMotifs(opts.motifs,nucFreqs,opts.motif_type)
preFilt = len(motifList)
motifList = filterMotifs(motifList,key=opts.motif_filter)
postFilt = len(motifList)
if opts.verbose: sys.stdout.write('using %s of %s motifs...\n' % (postFilt,preFilt))
if opts.verbose: sys.stdout.write('getting forgroundSeqs...\n')
foregroundSeqs = getForeground(opts.genes)
outData = {}
if opts.verbose: sys.stdout.write('calculating real data p-values...\n')
realData = motifHyprGeoEnrichmentTAMO(motifList,probeset,foregroundSeqs,factor=opts.thresh,bestFactor=False)
appendData(realData,outData)
for i in range(opts.fdrs):
if opts.verbose: sys.stdout.write('ctrl_%s:\n' % (i))
if opts.verbose: sys.stdout.write('\tgetting random forground...\n')
rForground = getRandomForground(foregroundSeqs,seqDict)
if opts.verbose: sys.stdout.write('\tcalculating p-values...\n')
ctrlData = motifHyprGeoEnrichmentTAMO(motifList,probeset,rForground,factor=opts.thresh,bestFactor=False)
appendData(ctrlData,outData)
if opts.verbose: sys.stdout.write('writting outData...\n')
writeDataTable(outBaseStr,outData,motifList)
if opts.verbose: sys.stdout.write('plotting histograms...\n')
for m in motifList:
plotHist(outBaseStr,outData,m.id)