[BioPython] script to extract records from nucleotide database

[Matthew Abravanel]

Hi everyone,

                  Sorry to keep going back to this script I am working on,
but I was wondering going back to what Peter said about my installation of
Bio-python that I think keeps messing up my code no matter what I do to
attempt to fix it. Could I use the "PortsCollection" to install bio-python
again since I am using BSD as my OS. I realize that you were only
speculation as to the nature of the problem with my install but do you think
that might work? Since I am not the one installing Bio-python and it is my
system administrator that is doing the installing I should talk to them
about it? 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
>