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 _from_sites(handle):
return Motif().from_jaspar_sites(handle)
def _from_pfm(handle):
return Motif().from_jaspar_pfm(handle)
