Biopython Developers List

bugzilla-daemon | 2 Jan 2009 02:37

[Bug 2544] Bio.GenBank and SeqFeature improvements

http://bugzilla.open-bio.org/show_bug.cgi?id=2544

------- Comment #4 from mmokrejs <at> ribosome.natur.cuni.cz  2009-01-01 20:37 EST -------
Can I instantiate GenBank file, reverse-complement the sequence (keep letter
casing) in the SeqIO object and dump it back to a GenBank file?

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bugzilla-daemon | 2 Jan 2009 19:15

[Bug 2544] Bio.GenBank and SeqFeature improvements

http://bugzilla.open-bio.org/show_bug.cgi?id=2544

------- Comment #5 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-02 13:15 EST -------
(In reply to comment #4)
> Can I instantiate GenBank file, reverse-complement the sequence
> (keep letter casing) in the SeqIO object and dump it back to a
> GenBank file?

I think this question would have been better handled on the mailing lists,
rather than on this bug.  Note that currently our GenBank output via Bio.SeqIO
does not include the features and references - see Bug 2294.

I would do this based on the approach described in the tutorial, which assumes
there could be many records in the input file.  Here is a variation for just
one record (untested):

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
record = SeqIO.read(open("example.gbk"), "genbank")
rc_record = SeqRecord(seq = record.seq.reverse_complement(), \
                      id = "rc_" + record.id, \
                      name = "rc_" + record.name, \
                      description = "reverse complement")
out_handle = open("rc_example.gbk","w")
SeqIO.write([rc_record], out_handle, "genbank")
out_handle.close()

Note you *could* override the record's sequence in situ:
record.seq = record.seq.reverse_complement() #BAD IDEA
This is a bad idea because none of the annotations will have been changed - in

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bugzilla-daemon | 3 Jan 2009 23:18

[Bug 2723] New: Clarify what applies to which version of biopython and other doc cleanup

http://bugzilla.open-bio.org/show_bug.cgi?id=2723

           Summary: Clarify what applies to which version of biopython and
                    other doc cleanup
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Documentation
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: mmokrejs <at> ribosome.natur.cuni.cz

I went to look around at the docs because the built-in tests of 1.49 setup.py
spitted some messages about external programs missing. I haven't found any
hints on them in http://news.open-bio.org/news/2008/11/biopython-release-149/.

Anyway, looking at 
http://biopython.org/DIST/docs/install/Installation.html#htoc17
I see: "3.4  mxTextTools (no longer needed)". I would propose:

3.4  mxTextTools (no longer needed since 1.49)

Similarly:
- 3.1  Numerical Python (NumPy) (strongly recommended)
+ 3.1  Numerical Python (NumPy) (strongly recommended since 1.49)

Bad URL links are in the text:

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bugzilla-daemon | 3 Jan 2009 23:30

[Bug 2724] New: Unclear? changes between 1.47 and 1.49

http://bugzilla.open-bio.org/show_bug.cgi?id=2724

           Summary: Unclear? changes between 1.47 and 1.49
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: mmokrejs <at> ribosome.natur.cuni.cz

I had a look by diff(1) what files were installed on my machine by 1.47 release
and which were installed by 1.49. I don't know what cdistance was about but the
mailing list archive search tool does not work, and searching for it manually
in raw archives of Oct and Nov 2008 did not help.

The second file shown here contains a white space in a filename, not critical
but maybe good to rename in next release.

-/usr/lib/python2.5/site-packages/Bio/cdistance.so
+/usr/share/biopython/Tests/Clustalw/temp horses.dnd

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bugzilla-daemon | 4 Jan 2009 02:10

[Bug 2724] Unclear? changes between 1.47 and 1.49

http://bugzilla.open-bio.org/show_bug.cgi?id=2724

------- Comment #1 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-03 20:10 EST -------
Bio.cdistance was an optional C implementation used within Bio.distance - the C
code was used if available to speed up calculations.  You can see the (now
deleted) code in CVS here:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Attic/cdistancemodule.c?hideattic=0&cvsroot=biopython

This C code (Bio.cdistance) was removed when the python code (Bio.distance) was
deprecated for release 1.49.

This was discussed at the start of October on the mailing list, see this
thread:
http://lists.open-bio.org/pipermail/biopython/2008-October/004532.html

This should have been mentioned in the DEPRECATED file, but wasn't.  I've
update this in CVS, see revision 1.41

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/DEPRECATED?cvsroot=biopython

Thanks for spotting this omission.

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bugzilla-daemon | 4 Jan 2009 02:20

[Bug 2724] Unclear? changes between 1.47 and 1.49

http://bugzilla.open-bio.org/show_bug.cgi?id=2724

biopython-bugzilla <at> maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Comment #2 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-03 20:20 EST -------
The file "/usr/share/biopython/Tests/Clustalw/temp horses.dnd" is normally
created by one of the unit tests, test_Clustalw_tool.py (and the space is very
deliberate).

This stray dnd file does appear to have been included with biopython-1.49.zip
(and probably the tar ball as well), which must have been a minor slip on my
part.  However, I don't think its worth re-issuing the archive files over this.

I've updated test_Clustalw_tool.py as of CVS revision 1.4 so that it should
remove this dnd file automatically.

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bugzilla-daemon | 4 Jan 2009 02:37

[Bug 2723] Clarify what applies to which version of biopython and other doc cleanup

http://bugzilla.open-bio.org/show_bug.cgi?id=2723

------- Comment #1 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-03 20:37 EST -------
(In reply to comment #0)
> I went to look around at the docs because the built-in tests of 1.49 setup.py
> spitted some messages about external programs missing. I haven't found any
> hints on them in http://news.open-bio.org/news/2008/11/biopython-release-149/.

No, that text and the matching email announcement don't do into details about
installation - the text was already long enough I felt.  However, the download
page does list various external programs:
http://biopython.org/wiki/Download

(Someone else had pointed out we were missing a few, which as been fixed, but I
couldn't find the email/bug report while writing this reply).

> Anyway, looking at 
> http://biopython.org/DIST/docs/install/Installation.html#htoc17
> I see: "3.4  mxTextTools (no longer needed)". I would propose:
> 
> 3.4  mxTextTools (no longer needed since 1.49)
> 
> Similarly:
> - 3.1  Numerical Python (NumPy) (strongly recommended)
> + 3.1  Numerical Python (NumPy) (strongly recommended since 1.49)

That does seem sensible.

> Bad URL links are in the text:
>

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bugzilla-daemon | 4 Jan 2009 19:56

[Bug 2723] Minor corrections to the installation document

http://bugzilla.open-bio.org/show_bug.cgi?id=2723

biopython-bugzilla <at> maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|Clarify what applies to     |Minor corrections to the
                   |which version of biopython  |installation document
                   |and other doc cleanup       |

------- Comment #2 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-04 13:56 EST -------
(In reply to comment #1)
> (In reply to comment #0)
> > I went to look around at the docs because the built-in tests of 1.49
> > setup.py spitted some messages about external programs missing. I haven't
> > found any hints on them in
> > http://news.open-bio.org/news/2008/11/biopython-release-149/.
> 
> No, that text and the matching email announcement don't do into details about
> installation - the text was already long enough I felt.  However, the download
> page does list various external programs:
> http://biopython.org/wiki/Download

I've added a section on third party tools to the installation document in CVS.

> > Anyway, looking at 
> > http://biopython.org/DIST/docs/install/Installation.html#htoc17
> > I see: "3.4  mxTextTools (no longer needed)". I would propose:
> > 
> > 3.4  mxTextTools (no longer needed since 1.49)

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bugzilla-daemon | 4 Jan 2009 23:09

[Bug 2671] Including GenomeDiagram in the main Biopython distribution

http://bugzilla.open-bio.org/show_bug.cgi?id=2671

------- Comment #32 from biopython-bugzilla <at> maubp.freeserve.co.uk  2009-01-04 17:09 EST -------
(In reply to comment #30)
> (In reply to comment #29)
> > 
> > I propose that in Biopython 1.50 we support both "colour" and "color",
> > but for Biopython 1.51 we add deprecation warnings when "colour" is used.
> > 
> > We should probably do the same thing for "centre" and "center" as well...
> > 
> 
> I agree.  We should encourage use of the US spelling in the documentation, to
> catch those new to GD. This approach provides a window for conversion of old
> GD scripts for previous users, which is a good thing.
> 

I've updated CVS to switch from centre to centre, with properties setup to
allow access under the old spellings, and where I thought it appropriate I've
included both spellings in argument lists.  Another set of eyes to check this
wouldn't hurt.

I'm leaving this bug open until we've done the documentation (see my comment
25).

There is also the issue of Bug 2705 for the AT and GC content and skew
functions and any windowing function to help plot these in GenomeDiagram.

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bugzilla-daemon | 5 Jan 2009 17:30

[Bug 2711] GenomeDiagram.py: write() and write_to_string() are inefficient and don't check inputs

http://bugzilla.open-bio.org/show_bug.cgi?id=2711

bsouthey <at> gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |

------- Comment #17 from bsouthey <at> gmail.com  2009-01-05 11:30 EST -------
I do not consider this bug completely fixed for multiple reasons of which my
patch addressed some of these prior to the creation of the _write function. I
do like where _write is heading as it is making cleaner and more understandable
code.

1) I do not understand the need for the dictionary of modules 'formatdict' in
_write as it creates unnecessary inefficient code. The options need to be part
of the check for the type of output.

2) There is no indication that the output for write and write_to_string only
accepts uppercase. Note the _write function states this but a user will not see
these. I do not understand why lowercase is unacceptable. 

3) The check for renderPM at start is really redundant because _write checks
for it (well sort of). It is also an unnecessary delay if renderPM is not used.
If you really must use the dictionary (which I really do not like) I would
suggest something like:
formatdict = {'PS': renderPS, 'PDF': renderPDF,'SVG': renderSVG}
try:
    from reportlab.graphics import renderPM

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