12.4. Parsing BLAST Output

So why parse BLAST output? One reason is to see if your DNA has any new matches against the DNA stored in the constantly growing databases. You can write a program to automatically perform a daily BLAST search and compare its results with those of the previous day by parsing the summary list of hits and comparing it with the previous day's summary list. You can then have the program email you if something new has turned up.

12.4.1. Extracting Annotation and Alignments

Example 12-1 consists of a main program and two new subroutines. The subroutines—parse_blast and parse_blast_alignment—use regular expressions to extract the various bits of data from a scalar string. I chose this method because the data, although structured, does not clearly identify each line with its function. (See the discussion in Chapter 10 and Chapter 11.)