class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = []
self.current_motif = None
self.param_dict = None
def parameters(self, line):
self.param_dict = {}
def parameter(self, line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name] = par_value
def sequences(self, line):
self.seq_dict = []
def sequence(self, line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self, line):
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self, line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self, line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self, line):
pass
def version(self, line):
self.ver = line
def command_line(self, line):
self.cmd_line = line
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = []
self.current_motif = None
self.param_dict = None
def parameters(self, line):
self.param_dict = {}
def parameter(self, line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name] = par_value
def sequences(self, line):
self.seq_dict = []
def sequence(self, line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self, line):
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self, line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self, line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self, line):
pass
def version(self, line):
self.ver = line
def command_line(self, line):
self.cmd_line = line
def createMaskedReferences(refFn, motifStr):
# Read input files
refRecs = [MaskedReference(rec) for rec in FastaReader(refFn)]
maskedMs = [Motif(m) for m in motifStr.split(',')] if motifStr else []
# Mask repeat regions
for motif in maskedMs:
for rec in refRecs:
rec.MaskRepeat(motif)
return refRecs
def do_globalAlignment(rep1, rep2):
# Aligment
align_dict = dict()
BASE = "rep1"
align_dict['rep1'] = alignment.pairwise_NW(rep1, rep1, 2, -1, -3, 1)[2]
align_dict['rep2'] = alignment.pairwise_NW(rep1, rep2, 2, -1, -3, 1)[2]
# get 'Match Matrix' and 'Gap List'
matchMatrix, gapSeqList = StructMatchGap3.structMatchGap(align_dict, BASE)
stageMatrixResult = StageMatrix.stageMatrix(matchMatrix, gapSeqList)
Motif_Obj = Motif(stageMatrixResult, BASE)
outputStage = OutputStage(stageMatrixResult, None, BASE, Motif_Obj)
executionTrace_dict = {"rep1": rep1, "rep2": rep2}
commonMotif = CommonMotif(stageMatrixResult, Motif_Obj,
executionTrace_dict, outputStage)
# comMotifdict= {'s<stage>_<motif>': [CMS], oriIdxRange1, oriIdxRange2},
comMotif_dict = commonMotif.getComMotifDict()
return comMotif_dict
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif(self,line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet=IUPAC.unambiguous_dna
def _from_sites(handle):
return Motif().from_jaspar_sites(handle)
def _from_pfm(handle):
return Motif().from_jaspar_pfm(handle)
def __init__(self):
Motif.__init__(self)
self.evalue = 0.0
def __init__ (self):
Motif.__init__(self)
self.evalue = 0.0