Esempio n. 1
0
 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
Esempio n. 3
0
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)