[Tutor] Biopython

[Alan Gauld]

On 10/04/12 21:25, Laura Scearce wrote:
> 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.

OK, That's not unusual and there is a forum somewhere for Python users 
doing bio type work. However, it helps if you tell us what distribution 
of Linux since their installers etc all work slightly differently (or 
more specifically there are three or four different installer packages 
that work differently across the dozens of Linux distros.)

> thought I would download Biopython, and am having troubles.

This is a list for people learning python. There may be people on the 
list that also know biopython but I wouldn't count on it. If you can 
find a biopython forum you are more likely to get useful help.

> 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

This means its trying to build from source. Does your PC have a
working development environment set up? Specifically can you
build C programs using make? If you don;t, or don;t know, you are 
probably out of your depth and should try to find a pre-built
package for your system.

> 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

OK, the fact that you are trying to  run sh on a tar.gz file tells me 
you are also a newbie to Linux as well as biopython.
You need to find the tool that your distro uses to open/install
"gunzip compressed tape archives" - which is what a tar.gz file is...

You can do it manually but thats likely to lead to even more problems if 
you don't really understand what you are doing.

You might be lucky and the distro has already set up the associations, 
what happens if you just run biopython-1.59.tar.gz? That might start the 
right tool automatically. Although what the tool will do depends on what 
is inside the archive.

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

You really are asking on the wrong forum.
First have you read this? I found it at the top ofd my first google 
search on biopython...

http://biopython.org/wiki/Biopython

There is a download and installation guide.

Also a page full of bio help sources:

http://biopython.org/wiki/Mailing_lists

In programming it always helps to read the manual first, it is 
invariably faster than guessing.

HTH,
-- 
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/