Its a pretty heterogeneous package for bioinformatics; there are lots
of modules that do lots of different things, written by different
people. Because of that, as with sage, there is some redundancy in
function that is slowly being weeded out. There are only about 5-10
very active developers at the moment though (at least that is my
impression). As the name implies, its all written in python. To some
extent, it imitates the more widely used BioPerl modules; perl has a
big lead in bioinformatics but I believe that is a historical artifact
and the superiority of python will eventually make it prevail :)
I mainly use it for its parsing and database functions - for example,
to retrieve a ferritin protein sequence from a 13-lined ground
squirrel (Spermophilus tridecemlineatus) from GenBank:
from Bio import SeqIO
from Bio import GenBank
gi_list = GenBank.search_for("Spermophilus[orgn] ferritin")
record_parser = GenBank.RecordParser()
ncbi_nuc_dict = GenBank.NCBIDictionary(database='nucleotide',
format='genbank', parser=record_parser)
record1 = ncbi_nuc_dict[gi_list[0]]
print record1.sequence
print record1.comment
...but there are lots of other functions for manipulating dna, rna,
and protein sequences, dealing with hidden markov models, 3D protein
databases and files, scoring matrices, neural networks, coalescence...
If that's not sufficient let me know.
-MH
On Dec 13, 7:03 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
> On Dec 13, 2007 4:27 PM, Marshall Hampton <[EMAIL PROTECTED]> wrote:
>
>
>
> > Excellent! Thank you!
>
> The only problem you might run into is if the optional biopython package
> is somehow "not relocatable", which would be a bug you should report
> here.
>
> By the way, could you describe from a sage point of view just what
> Biopython "is". It's something that takes only 15 seconds to install.
> What does it do, say in a paragraph or 2?
>
> William
>
>
>
> > On Dec 13, 5:30 pm, "William Stein" <[EMAIL PROTECTED]> wrote:
>
> > > On Dec 13, 2007 2:10 PM, Marshall Hampton <[EMAIL PROTECTED]> wrote:
>
> > > > The problem is that I am not the real administrator of the machines,
> > > > this is a one time thing.
>
> > > > The binaries appear to work, but now I need to install the biopython
> > > > package, which for some reason needs gcc. So I plan on installing the
> > > > xcode tools on one machine, and then copying the entire installation.
> > > > Is that a bad idea? I don't care if its crude if it works.
>
> > > Ah ha!! You're in luck. Just build biopython and any other packages you
> > > want
> > > into a copy of sage, then do
>
> > > sage -bdist 2.8.15-hampton-version
>
> > > and wait about 5 minutes. Then SAGE_ROOT/dist/ will contain a tarball
> > > sage-2.8.15-hampton-version.tar.gz
> > > that is suitable for install on all the other machines, and contains all
> > > your
> > > optional packages.
>
> > > William
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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