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