def scan_fa_with_motif_moods(fo,
motifs,
matrices,
bg,
thresholds,
nreport,
scan_rc=True):
scanner = MOODS.scan.Scanner(7)
scanner.set_motifs(matrices, bg, thresholds)
ret = []
for name, seq in fo.items():
l = len(seq)
scan_seq = seq.upper()
if scan_rc:
scan_seq = "".join((scan_seq, "N" * 50, rc(scan_seq)))
results = scanner.scan_max_hits(scan_seq, nreport)
for motif, result in zip(motifs, results):
matches = []
for match in result:
strand = 1
pos = match.pos
if scan_rc:
if pos > l:
pos = l - (pos - l - 50) - len(motif)
strand = -1
matches.append((pos, match.score, strand))
ret.append((motif, {name: matches}))
return ret
def scan_fa_with_motif_moods(fo, motifs, matrices, bg, thresholds, nreport, scan_rc=True):
scanner = MOODS.scan.Scanner(7)
scanner.set_motifs(matrices, bg, thresholds)
ret = []
for name, seq in fo.items():
l = len(seq)
scan_seq = seq.upper()
if scan_rc:
scan_seq = "".join((scan_seq, "N"*50, rc(scan_seq)))
results = scanner.scan_max_hits(scan_seq, nreport)
for motif,result in zip(motifs, results):
matches = []
for match in result:
strand = 1
pos = match.pos
if scan_rc:
if pos > l:
pos = l - (pos - l - 50) - len(motif)
strand = -1
matches.append((pos, match.score, strand))
ret.append((motif, {name: matches}))
return ret
def scan_fa_with_motif_moods_count(fo, motifs, matrices, bg, thresholds, nreport, scan_rc=True):
scanner = MOODS.scan.Scanner(7)
scanner.set_motifs(matrices, bg, thresholds)
ret = []
for name, seq in fo.items():
l = len(seq)
scan_seq = seq.upper()
if scan_rc:
scan_seq = "".join((scan_seq, "N"*50, rc(scan_seq)))
results = scanner.counts_max_hits(scan_seq, nreport)
ret.append((name, results))
return ret
def scan_fa_with_motif_moods_count(fo,
motifs,
matrices,
bg,
thresholds,
nreport,
scan_rc=True):
scanner = MOODS.scan.Scanner(7)
scanner.set_motifs(matrices, bg, thresholds)
ret = []
for name, seq in fo.items():
l = len(seq)
scan_seq = seq.upper()
if scan_rc:
scan_seq = "".join((scan_seq, "N" * 50, rc(scan_seq)))
results = scanner.counts_max_hits(scan_seq, nreport)
ret.append((name, results))
return ret
