def _score_splice_site(seq,splicetype="donor"):
"""
Return PSSM splice site score
@type seq: string
@param seq: DNA sequence of EXACT length of the PSSM
@type splicetype: string
@param splicetype: 'donor' or 'acceptor'
@rtype: float
@return: PSSM score for this splice site
"""
if splicetype=='acceptor':
return pssmscore(seq,IC_ACCEPTOR)
else:
if seq[IC_DONOR_PATTERN_OFFSET[0]:-IC_DONOR_PATTERN_OFFSET[-1]].upper() == "GC":
return pssmscore(seq,IC_NC_GC_DONOR)
else:
return pssmscore(seq,IC_DONOR)
def score_tss(seq,ignore_unambiguity=False):
"""
Return PSSM TSS score
@type seq: string
@param seq: DNA sequence of EXACT length of the PSSM
@rtype: float
@return: PSSM score for this TSS (translational start site)
"""
return pssmscore(seq,IC_TSS,ignore_unambiguity=ignore_unambiguity)
def _score_splice_site(seq, splicetype="donor"):
"""
Return PSSM splice site score
@type seq: string
@param seq: DNA sequence of EXACT length of the PSSM
@type splicetype: string
@param splicetype: 'donor' or 'acceptor'
@rtype: float
@return: PSSM score for this splice site
"""
if splicetype == 'acceptor':
return pssmscore(seq, IC_ACCEPTOR)
else:
if seq[IC_DONOR_PATTERN_OFFSET[0]:-IC_DONOR_PATTERN_OFFSET[-1]].upper(
) == "GC":
return pssmscore(seq, IC_NC_GC_DONOR)
else:
return pssmscore(seq, IC_DONOR)
