[BioPython] Bug 2393 in bugzilla for the Bio.GenBank.NCBIDictionary code

[Matthew Abravanel]

Hi all,

I was wondering not being familiar with the bugzilla feature, if  I wanted
to fix Bug 2393 there seems to be a patch with the .py extention that was
created for it. Do I need to download that file or type it into my existing
code or something like that?  Please excuse my ignorence. Thanks.

 Matthew

On Nov 15, 2007 2:11 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> > Thanks for all the comments, so since you said you removed Bio.FormatIOin
> > version 1.44 and replaced it with Bio.SeqIO do you think I can still
> > successfully use that code I was given if I have 1.44 provided I watch
> out
> > for bugs and so on?
>
> Assuming you can apply the fix for Bug 2393, then that
> Bio.GenBank.NCBIDictionary code should work fine with Biopython 1.44.
>
> There is also a related example in the SeqIO chapter of the tutorial
> using the Bio.GenBank.download_many() function.
>
> > What is the difference between Bio.FormatIO and
> > Bio.SeqIO, other then them describing file formats differently?
>
> In terms of typical end use, Bio.SeqIO and Bio.FormatIO provided
> similar capabilities, but FormatIO wasn't very up to date in terms of
> its format support.  The big differences are internal.  For any new
> code, please try Bio.SeqIO (available in Biopython 1.43 onwards),
> which is described in the tutorial and the wiki:
> http://biopython.org/wiki/SeqIO
>
> > Also how exactly could one have a partial installation, some of the
> package not
> > installing?
>
> This was a guess - there is/was clearly something odd about your
> install.  If you installed from source, maybe some step failed part
> way leaving you with only some parts installed.  Another possibility
> is on BSD is there is something different about the installation paths
> which is confusing things.  We haven't worked out what went wrong on
> your system so I'm was just speculating.
>
> Peter
>