def __init__(self, donor, acceptor, shared_nts, gff={}):
self.donor = donor
self.acceptor = acceptor
self.length = acceptor.pos - donor.pos
self.start = donor.pos
self.end = acceptor.pos
self.phase = None
self.nt_from_stop_donor = None
self.nt_from_stop_acceptor = None
# check/set phase of the intron
if self.donor.phase and self.acceptor.phase:
if self.donor.phase == self.acceptor.phase:
self.phase = self.donor.phase
else:
raise IncompatibleSpliceSitePhases
elif self.donor.phase == 0 and self.acceptor.phase == 0:
self.phase = 0
else:
# hmm... not recommended, but no phase specified on donor/acceptor
pass
# set/update gff data
self._gff = {
'fref': None,
'fscource': 'undefined',
'fstrand': '+',
'fscore': ".",
'column9data': {},
}
self._gff.update(gff)
# and set some shared nt/aa data
self.shared_nts = shared_nts
self.shared_aa = ""
if self.shared_nts:
self.shared_aa = dna2prot.dna2protein(self.shared_nts)
def dna2protein(_sequence,_frame):
"""
Translate a DNA sequence into AAs for a given frame
@type _sequence: string
@param _sequence: DNA seqeunce string
@type _frame: integer
@param _frame: desired reading frame (0,1,2)
@rtype: string
@return: Protein sequence
"""
_untill = (len(_sequence)-_frame) % 3
if not _untill: _untill = len(_sequence)
else: _untill = -_untill
# and do the actual translation
return dna2prot.dna2protein(_sequence[_frame:_untill])
def _get_reverse_strand_coords_and_seqs(dnaseq, start, end):
"""
TODO ....
@type dnaseq: string
@param dnaseq: DNA sequence string
@type start: integer
@param start:
@type end: integer
@param end:
@rtype: tuple
@return: (start,end,dnarevseq,protseq)
"""
# obtain position of the exterior stop codons on the other strand
# take care with EOF sequence; after while loop +3; so stop at -6 end
if end >= len(dnaseq) - 6:
# end offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while end >= len(dnaseq) - 3:
end -= 3
else:
while end < len(dnaseq) - 6:
if dnaseq[end:end + 3].upper() in REV_STOP_CODONS: break
end += 3
# take care with EOF sequence; after while loop -3; so stop at +6 end
if start < 6:
# start offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while start < 3:
start += 3
else:
while start >= 6:
if dnaseq[start - 3:start].upper() in REV_STOP_CODONS: break
start -= 3
# get DNA & Protein sequences on the reverse strand
start -= 3
end += 3
dnarevseq = _reversecomplement(dnaseq[start:end])
protseq = dna2protein(dnarevseq)
# return coords & sequences
return (start, end, dnarevseq, protseq)
def _get_reverse_strand_coords_and_seqs(dnaseq,start,end):
"""
TODO ....
@type dnaseq: string
@param dnaseq: DNA sequence string
@type start: integer
@param start:
@type end: integer
@param end:
@rtype: tuple
@return: (start,end,dnarevseq,protseq)
"""
# obtain position of the exterior stop codons on the other strand
# take care with EOF sequence; after while loop +3; so stop at -6 end
if end >= len(dnaseq)-6:
# end offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while end >= len(dnaseq)-3: end-=3
else:
while end < len(dnaseq)-6:
if dnaseq[end:end+3].upper() in REV_STOP_CODONS: break
end += 3
# take care with EOF sequence; after while loop -3; so stop at +6 end
if start < 6:
# start offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while start < 3: start += 3
else:
while start >= 6:
if dnaseq[start-3:start].upper() in REV_STOP_CODONS: break
start -= 3
# get DNA & Protein sequences on the reverse strand
start-=3
end+=3
dnarevseq = _reversecomplement(dnaseq[start:end])
protseq = dna2protein(dnarevseq)
# return coords & sequences
return (start,end,dnarevseq,protseq)
def __init__(self,donor,acceptor,shared_nts,gff={}):
# input validation
IsDonor(donor)
IsAcceptor(acceptor)
# initialization
BasicGFF.__init__(self)
self._gff.update(gff)
self.donor = donor
self.acceptor = acceptor
# init by splice site objects
self._init_by_splicesites()
# forward compatibility with IntronConnectingOrfs
self.nt_from_stop_donor = None
self.nt_from_stop_acceptor = None
# set shared nt/aa data
self.shared_nts = shared_nts
self.shared_aa = ""
if self.shared_nts:
self.shared_aa = dna2prot.dna2protein(self.shared_nts)
if not exons:
for track in input[k]['gff-gene']: print track
for warn in input[k]['warnings']:
print "\t", warn
print ""
# check if the DNA exon structure equals the given protein sequence (None|True|False)
from dna2prot import dna2protein
print "# test if annotated gene model equals provided protein sequence in AbfgpGeneLocusDirectory"
for k in input.keys():
exons = input[k]['gldobj'].as_exons()
seqp = []
for item in exons:
if item.__class__.__name__.find('Exon') >= 0:
seqp.append( item.dnasequence() )
_trans = dna2protein("".join(seqp))
_prot = input[k]['proteinseq'].replace('*','')
if not _prot:
print None, "\t", k
continue
else:
print _trans == _prot, "\t", k
if dna2protein("".join(seqp))!=input[k]['proteinseq'].replace('*',''):
translated = dna2protein("".join(seqp))
for offset in range(0,len(input[k]['proteinseq']),100):
_trans = translated[offset:offset+100]
_prot = input[k]['proteinseq'][offset:offset+100].replace("*","")
print "prot:", input[k]['proteinseq'][offset:offset+100]
print "gene:", translated[offset:offset+100],
print _trans == _prot