def makePWMscorefiles(fastafiles, pwmfiles, destdir, both_strands=True):
for fastaf in fastafile:
thisseqname = fastaf.split('/')[-1].split('.')[0]
handle = open(fastaf, "r")
records = list(Bio.SeqIO.parse(handle, "fasta"))
handle.close()
thisseq = records[0].seq
print 'Doing sequence ', thisseqname, 'length=', len(thisseq)
for pwmf in pwmfiles:
thispwmname = pwmf.split('/')[-1]
print ' Doing pwm ', thispwmname
thispwm = MOODS.load_matrix(pwmf)
thispwmcomplement = MOODS.reverse_complement(thispwm)
print ' strand 1'
onestrandindexvector=getMOODSscore(thisseq, thispwm)
print ' strand 2'
otherstrandindexvecor=getMOODSscore(thisseq, thispwmcomplement)
print ' finding best score per bp'
bothstrandsindexvector = np.append( onestrandindexvector, otherstrandindexvecor, axis=0)
bestscorevector = getMaxPWMScore( bothstrandsindexvector, len(thispwm[0]))
for strandnbr in range(len(bothstrandsindexvector)):
print ' writing wiggle for strand', str(strandnbr)
vegardswritewiggle(bothstrandsindexvector[strandnbr,:], name=thispwmname, chr=thisseqname, destpath=destdir + '/' + 'start_index_score/'+ thispwmname+ '/strand_'+str(strandnbr))
print ' writing wiggle for bestscore'
vegardswritewiggle(bestscorevector, name=thispwmname, chr=thisseqname, destpath=destdir + '/' + 'best_score_in_window/'+thispwmname)
def getMOODSscore(seqfile, pwmfiles, both_strands=False):
handle = open(seqfile, "r")
records = list(Bio.SeqIO.parse(handle, "fasta"))
handle.close()
seq = records[0].seq
print 'len(seq)=', len(seq)
matrixlist = list()
for f in pwmfiles:
matrix = MOODS.load_matrix(f)
print 'pwm ', f, 'windowlength=', len(matrix[0])
matrixlist.append(matrix)
if both_strands:
matrixlist.append(
MOODS.reverse_complement(matrix)
) # both_strand option in MOODS returned a akward result.
print 'starting MOODS.search', datetime.now()
results = MOODS.search(seq,
matrixlist,
thresholds=1,
absolute_threshold=False)
print 'done MOODS.search', datetime.now()
reslist = []
for n in range(len(pwmfiles)):
thisind = n * (1 + both_strands)
reslist.append(vegardparseMOODSres(results[thisind], len(seq)))
if both_strands:
reslist[n] = np.append(reslist[n],
vegardparseMOODSres(results[thisind + 1],
len(seq)),
axis=0)
return (reslist)
def getMOODSscore(seqfile, pwmfiles, both_strands=False):
handle = open(seqfile, "r")
records = list(Bio.SeqIO.parse(handle, "fasta"))
handle.close()
seq = records[0].seq
print 'len(seq)=',len(seq)
matrixlist=list()
for f in pwmfiles:
matrix = MOODS.load_matrix(f)
print 'pwm ', f , 'windowlength=', len(matrix[0])
matrixlist.append(matrix)
if both_strands:
matrixlist.append(MOODS.reverse_complement(matrix)) # both_strand option in MOODS returned a akward result.
print 'starting MOODS.search', datetime.now()
results = MOODS.search(seq, matrixlist, thresholds=1, absolute_threshold=False)
print 'done MOODS.search', datetime.now()
reslist=[]
for n in range(len(pwmfiles)):
thisind = n * (1 + both_strands)
reslist.append(vegardparseMOODSres( results[thisind] , len(seq)))
if both_strands:
reslist[n] = np.append( reslist[n] , vegardparseMOODSres( results[thisind+1] , len(seq)), axis=0)
return(reslist)
for i in results:
for (position, score) in i:
print("Position: " + str(position) + " Score: "+ str(score))
print('one way')
results = MOODS.search(teststring, [matrix], thresholds=1, absolute_threshold=False, both_strands=False)
for i in results:
for (position, score) in i:
print("Position: " + str(position) + " Score: "+ str(score))
print('other way')
results = MOODS.search(teststring, [ ,MOODS.reverse_complement(matrix)], thresholds=1, absolute_threshold=False, both_strands=False)
results = MOODS.search(teststring, [ matrix , matrix], thresholds=1, absolute_threshold=False, both_strands=False)
MOODS.search(teststring, [ matrix ], thresholds=1, absolute_threshold=False, both_strands=True)
for i in results:
for (position, score) in i:
print("Position: " + str(position) + " Score: "+ str(score))
# /xanadu/home/vegardny/prosjekter/hyperbrowser/pwm_vs_snp/MOODS/src/find_pssm_dna 1 -algorithm=naive /xanadu/home/vegardny/prosjekter/hyperbrowser/pwm_vs_snp/vegard_debug_MOODS/examples/vegardtest2.fasta /xanadu/home/vegardny/prosjekter/hyperbrowser/pwm_vs_snp/vegard_debug_MOODS/examples/vegardtest2.pfm
