blast-wordcloud

Is a Python program that uses the word_cloud package to create word cloud PNG images from words in sequence titles matched by a BLAST search.

Usage

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

Then:

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

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

Use

$ blast-wordcloud.py --help

to see additional arguments.

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 and 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).

Then:

$ pip install -r requirements.txt