def __get__(self, obj, objtype):
'''Concatenate exon sequences of a transcript to obtain
its sequence.'''
exon_count = obj.exonCount
exon_starts = obj.exonStarts.split(',')[:exon_count]
exon_ends = obj.exonEnds.split(',')[:exon_count]
trans_seq = ''
for i in range(0, exon_count):
trans_seq += str(
sequence.absoluteSlice(obj._anno_seq, int(exon_starts[i]),
int(exon_ends[i])))
seq = sequence.Sequence(trans_seq, obj.name)
setattr(obj, self.attr, seq) # cache on object
return seq
def __get__(self, obj, objtype):
'''Concatenate exon sequences of a transcript to obtain
its sequence.'''
exon_count = obj.exonCount
exon_starts = obj.exonStarts.split(',')[:exon_count]
exon_ends = obj.exonEnds.split(',')[:exon_count]
trans_seq = ''
for i in range(0, exon_count):
trans_seq += str(sequence.absoluteSlice(obj._anno_seq,
int(exon_starts[i]),
int(exon_ends[i])))
seq = sequence.Sequence(trans_seq, obj.name)
setattr(obj, self.attr, seq) # cache on object
return seq
def printSliceAlignment(myslice, ifile=None):
"""print alignment of a gene as text, with numbering,
seq differences in bold. Suitable for viewing as .html file in a browser..."""
from pygr import sequence
if ifile is None:
import sys
ifile = sys.stdout
d = Autodict(myslice.stop - myslice.start)
namedict = ~(myslice.nlmsaSequence.nlmsaLetters.seqDict)
writeSeqToArray(myslice.start, 0, sequence.absoluteSlice(myslice.seq, myslice.start, myslice.stop), d, namedict)
numline = d["#"]
i = (myslice.start + 19) - ((myslice.start + 19) % 20)
while i < myslice.stop:
writeNumToArray(i, myslice.start, numline)
i += 20
for srcPath, destPath, t in myslice.edges():
writeSeqToArray(destPath.start, srcPath.start - myslice.start, destPath, d, namedict)
printHTML(d, ifile, 100)