biopython 1.24

Freely available tools for computational molecular biology.

**Biopython README file**

"The Biopython Project":http://www.biopython.org/ is an
international association of developers of freely available Python
tools for computational molecular biology.

biopython.org provides an online resource for modules, scripts, and
web links for developers of Python-based software for life science
research. Thanks to bioperl, we can also provide web, FTP and CVS
space for individuals and organizations wishing to distribute or
otherwise make available standalone scripts & code.

This Biopython package is made available under generous terms. Please
see the LICENSE file for further details.


**For the impatient**

To build and install Biopython, type:
python setup.py build
python setup.py test
python setup.py install


**System Requirements**

o "Python 2.2 or better":http://www.python.org/

o "mxTextTools":http://starship.python.net/~lemburg/mxTextTools.html
This is used in many of the text handling routines in Biopython.
Much of Biopython will not work without it.

o "Numerical Python":http://numpy.sourceforge.net/ (optional)
This package is only used in the computationally-oriented modules.
It is required for Bio.Cluster and a few other modules. If you
think you might need these modules, then please install Numeric
Python first. Also, please install if you are seeing
error messages such as:
ImportError: No module named Numeric

o ReportLab (optional)
This package is used in some code that generates graphical displays
of chromosomes. If you do not need this functoinality, you will not
need to install this package.

o psycopg:http://initd.org/software/psycopg/ (optional)
This package is only used by BioSQL to access a PostgreSQL database.

o MySQLdb:http://sourceforge.net/projects/mysql-python (optional)
This package is only used by Bio.GFF to access a MySQL database.


**Installation**

*** Make sure Python and Distutils are installed correctly ***

Installation should be as simple as going to the biopython directory,
and typing:

'python setup.py install'


If you need to do additional configuration, e.g. changing the base
directory, please type 'python setup.py', or see the documentation for
Distutils.


For FreeBSD users, "Johann Visagie", mailto:[e-mail] has made
Biopython available in the ports tree. According to Johann:

This means that a FreeBSD user with an up-to-date ports tree can now
install BioPython as simply as:

'cd /usr/ports/biology/py-biopython ; make install'

Fetching of the package as well as installation of all dependencies
(Python itself as well as Distutils) will be handled automagically.


We have been noticing some problems building the _KDTreecmodule
extension on some platforms (e.g. Solaris). If you see lots of error
messages followed by:
ld: fatal: relocations remain against allocatable but non-writable sections

you may be having this error. We are trying to track this down. In
the meantime, you can disable this module by commenting out the
following lines in the setup.py file:
Extension('Bio.KDTree._KDTreecmodule',
["Bio/KDTree/_KDTree.C",
"Bio/KDTree/_KDTree.swig.C"],
libraries=["stdc++"]
),
This module is commented out by default now -- so please uncomment if you
want to install and use it.
The rest of Biopython will build and run fine.


**Testing**

Biopython includes a suite of regression tests to check if
everything's running correctly. To do the tests, type:
drevil:~/biopython> python setup.py test

If you have Tk installed, this will run a nice GUI that displays the
results of the tests. Otherwise, you will see results on the command
line.

Do not panic if you see messages warning of skipped tests:
Skipping test because of import error: No module named reportlab.pdfgen

This most likely means that a package is not installed. You can
ignore this if it occurs in the tests for a module that you were not
planning on using. If you did want to use that module, please install
the required dependency and re-run the tests.


**Bugs**

While we try to ship a robust package, bugs inevitably pop up. If you
are having problems that might be caused by a bug in Biopython, it is
possible that it has already been identified. Search the
"bug database":http://bugzilla.open-bio.org/ and mailing lists
to see if it has already been reported (and hopefully fixed).

If you suspect the problem lies within a parser, it is likely that the
data format has changed and broken the parsing code. (The BLAST and
GenBank formats seem to be particularly fragile.) Thus, the parsing
code in Biopython is updated faster than we can build Biopython
releases. You can get the most recent parser by pulling the relevant
files (e.g. genbank_format.py) out of
"anonymous cvs":http://cvs.biopython.org/ .
However, be careful when doing this, because the code in CVS is not as
well-tested as released code, and may contain new dependencies.

Finally, you can send a bug report to the bug database or
[e-mail]. In the bug report, please let us know 1)
which operating system and hardware you are using, 2) Python version,
3) Biopython version (or CVS version/date), 4) traceback that occurs,
5) offending code, and 6) data file that causes the problem.



**Contributing, Bug Reports**

Biopython is run by volunteers from all over the world, with many
types of backgrounds. We are always looking for people interested in
helping with code development, web-site management, documentation
writing, technical administration, and whatever else comes up.

If you wish to contribute, please visit the
"web site":http://www.biopython.org
and join our "mailing list":http://biopython.org/maillists/



**Distribution Structure**

README -- This file.

NEWS -- Release notes and news

LICENSE -- What you can do with the code.

CONTRIB -- An (incomplete) list of people who helped Biopython in
one way or another.

MANIFEST.in -- Tells distutils what files to distribute

setup.py -- Installation file.

Bio/ -- The main code base code.

Martel/ -- Code for the Martel parsing system, used in many Biopython parsers.

BioSQL/ -- Code for using Biopython with BioSQL databases.

Doc/ -- Documentation.

Scripts/ -- Miscellaneous, possibly useful, standalone scripts

Tests/ -- Regression testing code