[Biopython-dev] MetaTool

[Cayte]

I plan to fix metatool in a day or two when I go to the lake island where I
have my new linux system to run
the tests It looks like there is an extraneous file that is not part of the
tests.  It should not cause tests to fail but it may confuse users.

                            Cayte>
>
>
>
> On Tue, Jul 16, 2002 at 03:23:46PM -0700, daishi at egcrc.net wrote:
> > Jeffrey Chang wrote:
> > > Hi Daishi,
> > >
> > > Thanks for the bug report and patch.  I will look into this soon.
> > >
> > > Jeff
> >
> > Please ignore the previous patch; it contains a bug.
> > I believe I now understand the purpose of L332-333;
> > I have reincorporated the functionality in a slightly
> > different way which works with my other modifications.
> > The new patch follows:
> >
> > *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul  9
15:08:53 2002
> > --- fastpairwise.py Tue Jul 16 15:15:50 2002
> > ***************
> > *** 302,308 ****
> >            else:
> >                # Since the length of the alignment is unknown, set an
> >                # offset from the end of the alignment.
> > !             begin, end = 0, -len(seqA)
> >                if not end:
> >                    end = None
> >            x = seqA, seqB, score, begin, end, row, col, []
> > --- 302,308 ----
> >            else:
> >                # Since the length of the alignment is unknown, set an
> >                # offset from the end of the alignment.
> > !             begin, end = None, -len(seqA)
> >                if not end:
> >                    end = None
> >            x = seqA, seqB, score, begin, end, row, col, []
> > ***************
> > *** 326,341 ****
> >                    elif col < 0:
> >                        begin = row + 1
> >                for cseqA, cseqB, cbegin, taillen in path_cache[(row,
col)]:
> > !                 nbegin = begin
> >                    nseqA = cseqA[:-taillen] + seqA
> >                    nseqB = cseqB[:-taillen] + seqB
> > !                 if nbegin < cbegin:
> > !                     nbegin = cbegin
> >                    x = nseqA, nseqB, score, nbegin, end, -1, -1, path
> >                    in_process.append(x)
> >            elif row < 0 and col < 0:
> >                # This one is done.  Put it into the tracebacks list and
> >                # continue.
> >                tracebacks.append((seqA, seqB, score, begin, end))
> >                path.pop()   # Don't cache the last step.
> >                # Update the cache.
> > --- 326,346 ----
> >                    elif col < 0:
> >                        begin = row + 1
> >                for cseqA, cseqB, cbegin, taillen in path_cache[(row,
col)]:
> > !                 if begin:
> > !                     nbegin = begin
> > !                 else:
> > !                     nbegin = cbegin
> >                    nseqA = cseqA[:-taillen] + seqA
> >                    nseqB = cseqB[:-taillen] + seqB
> > ! #                if nbegin < cbegin:
> > ! #                    nbegin = cbegin
> >                    x = nseqA, nseqB, score, nbegin, end, -1, -1, path
> >                    in_process.append(x)
> >            elif row < 0 and col < 0:
> >                # This one is done.  Put it into the tracebacks list and
> >                # continue.
> > +             if not begin:
> > +                 begin = 0
> >                tracebacks.append((seqA, seqB, score, begin, end))
> >                path.pop()   # Don't cache the last step.
> >                # Update the cache.
> > ***************
> > *** 347,360 ****
> >            elif row < 0:
> >                nseqA = gap_char + seqA
> >                nseqB = sequenceB[col:col+1] + seqB
> > !             if not global_alignment:
> >                    begin = col + 1
> >                x = nseqA, nseqB, score, begin, end, row, col-1, path
> >                in_process.append(x)
> >            elif col < 0:
> >                nseqA = sequenceA[row:row+1] + seqA
> >                nseqB = gap_char + seqB
> > !             if not global_alignment:
> >                    begin = row + 1
> >                x = nseqA, nseqB, score, begin, end, row-1, col, path
> >                in_process.append(x)
> > --- 352,365 ----
> >            elif row < 0:
> >                nseqA = gap_char + seqA
> >                nseqB = sequenceB[col:col+1] + seqB
> > !             if not (global_alignment or begin):
> >                    begin = col + 1
> >                x = nseqA, nseqB, score, begin, end, row, col-1, path
> >                in_process.append(x)
> >            elif col < 0:
> >                nseqA = sequenceA[row:row+1] + seqA
> >                nseqB = gap_char + seqB
> > !             if not (global_alignment or begin):
> >                    begin = row + 1
> >                x = nseqA, nseqB, score, begin, end, row-1, col, path
> >                in_process.append(x)
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