This is a Python program to display word clouds based on the titles that are matched by BLAST.

Usage

First, run blast and use -outfmt 5 on the command line to get XML output. Let's suppose that's in a file called blast-output.xml. Then:

$ blast-wordcloud.py --in blast-output.xml --out word-cloud.png

In this example, your word cloud image will be saved to word-cloud.png.

If the BLAST database you're matching against was downloaded from NCBI, you'll likely find the --ncbiTitles option useful. That will transform an NCBI sequence title like "gi|361057412|gb|CP003178.1| Niastella koreensis, complete genome" into "Niastella koreensis". It uses a simple heuristic - only keep the text between the first space and the first comma in the title, but it is quite effective.

Installing under Linux

You'll need Python installed, which should already be the case. You might want to make a virtualenv for the installation (otherwise you'll need to run the following using sudo, which isn't recommended).

Firstly pip install -r requirements.txt.

Then install Pygame from here.

Installing under Mac OS X

You'll need Python installed, which should already be the case. You might want to make a virtualenv for the installation (otherwise you'll need to run the following using sudo, which isn't recommended).

Firstly, pip install -r requirements.txt.

Installing pygame

Unfortunaely this is quite awkward, and I haven't managed to make it work. I have brew's X11 installed, and I did the following:

• Download and unpack the pygame 1.9.1 sources from here

• $ python setup.py install

• This fails on a compile (unable to find X11/Xlib.h). Edit the Setup file that was created by the failed install, and add -I/opt/X11/include to the end of the SDL = ... line at the top.

• Edit src/scale_mmx64.c and change the two instances of movsxl to be movslq see here for some details on that.

• For Python 2.7 I had to run $ sudo mkdir ~/.virtualenvs/lm/include/python2.7/pygame and $ sudo chown $USER ~/.virtualenvs/lm/include/python2.7/pygame. That's because the Brew python 2.x links to the system python, so the above directory is actually in /System/Library/Frameworks/Python.framework/Versions/2.7.

• Re-run $ python setup install. If all goes well you should then be able to cleanly run $ python -c 'import pygame'.

Problem under Python 2

Although pygame can now be imported, it doesn't fully work. Under Python2 I get an error from pygame.font.init():

$ python
Python 2.7.10 (default, Jul 14 2015, 19:46:27)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Jedi is not installed, falling back to readline
>>> import pygame
>>> pygame.init()
/Users/terry/.virtualenvs/lm/lib/python2.7/site-packages/pygame/pkgdata.py:27: UserWarning: Module pygame was already imported from /Users/terry/.virtualenvs/lm/lib/python2.7/site-packages/pygame/__init__.pyc, but /private/tmp/pygame-1.9.1release is being added to sys.path
  from pkg_resources import resource_stream, resource_exists
(4, 0)
>>> pygame.font.init()
__main__:1: RuntimeWarning: use font: No module named font
(ImportError: No module named font)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/terry/.virtualenvs/lm/lib/python2.7/site-packages/pygame/__init__.py", line 70, in __getattr__
    raise NotImplementedError(MissingPygameModule)
NotImplementedError: font module not available
(ImportError: No module named font)

There are some pages on the web that implicate a mix of 32-bit and 64-bit Python for the above, but I don't know how any 32-bit stuff can be happening on my machine.

Unfortunately, pytagcloud makes heavy use of pygame (at least it imports many things).

Problem under Python 3

Under Python 3.5 there is a different error:

$ python -c 'import pygame'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/terry/.virtualenvs/lm35/lib/python3.5/site-packages/pygame/__init__.py", line 95, in <module>
    from pygame.base import *
ImportError: dlopen(/Users/terry/.virtualenvs/lm35/lib/python3.5/site-packages/pygame/base.cpython-35m-darwin.so, 2): Symbol not found: _PyCObject_AsVoidPtr
  Referenced from: /Users/terry/.virtualenvs/lm35/lib/python3.5/site-packages/pygame/base.cpython-35m-darwin.so
  Expected in: flat namespace
 in /Users/terry/.virtualenvs/lm35/lib/python3.5/site-packages/pygame/base.cpython-35m-darwin.so

I'm not sure what's going on here, but have checked to make sure base.cpython-35m-darwin.so exists (it does) and that it doesn't contain _PyCObject_AsVoidPtr (it doesn't - you can check with nm -a).

Some googling is required, I guess. But we may never get there on modern Mac OS X. The last release of pygame was from 2009 :-(