[Tutor] Biopython

[Laura Scearce]

Hello,
I am using Linux version 2.6 and python version 2.6.6 (gcc version 4.4.5).
I have a list of protein names and am trying to get their sequences. I
thought I would download Biopython, and am having troubles.
I first downloaded and installed easyinstall from
http://pypi.python.org/pypi/setuptools
I followed the instructions and it seemed to work (see below error
messages).

This is the error I get when I try to install biopython:
root at debbie-VirtualBox:/usr/local/bin# easy_install biopython
Searching for biopython
Reading http://pypi.python.org/simple/biopython/
Reading http://www.biopython.org/
Reading http://biopython.org/DIST/
Best match: biopython 1.59
Downloading http://biopython.org/DIST/biopython-1.59.zip
Processing biopython-1.59.zip
Running biopython-1.59/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-qMfJsF/biopython-1.59/egg-dist-tmp-W4L1YX
warning: no previously-included files found matching 'Tests/Graphics/*'
warning: no previously-included files matching '.cvsignore' found under
directory '*'
warning: no previously-included files matching '*.pyc' found under
directory '*'
Bio/cpairwise2module.c:12: fatal error: Python.h: No such file or directory
compilation terminated.
error: Setup script exited with error: command 'gcc' failed with exit
status 1

*I also tried it in the directory Downloads, because this is where the
easyinstall was downloaded to. Same message.

Then I tried downloading Biopython from
http://pypi.python.org/pypi/biopython
I downloaded biopython-1.59.tar.gz<http://pypi.python.org/packages/source/b/biopython/biopython-1.59.tar.gz#md5=c83b26cc1bc2b2ecdce28c1b5e49110d>.
and extracted it to the folder BLAST-SW in my Documents folder.

Here is what I tried:
debbie at debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59.tar.gz
sh: Can't open biopython-1.59.tar.gz
debbie at debbie-VirtualBox:~$ sh biopython-1.59.tar.gz
sh: Can't open biopython-1.59.tar.gz
debbie at debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59
*This had no error message, but I think that Biopython is not installed
because:
>>> import Bio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named Bio

The end goal is to use ncbi Eutils to get protein sequences, so if anyone
has experience with this please let me know.
Thanks!
Laura Scearce
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