Genomics (Ecol 553) Computational Lab
Week 13: Nov 14, 2006.
Course webpage: http://genomics.arizona.edu/553/computation
Homework8
To be completed by noon on Tuesday, Nov 21.
On amadeus, create a directory called ~/homework/homework8. Place the program described below into this directory. ** Do not make copies of the input files into your directory. **
1) Write a program, called parse_longform_blast.pl, which does the following:
*
Using bioperl, reads in the file at /tmp/week13/blast_longform.out
* For each query sequence,
* identify the hsp that covers the greatest length of that
query sequence (there may be more than one with the same maximum length
- pick one)
( how much of the query
sequence is covered by an hsp? See bioperl docs: $len =
$hsp->length( 'query' );
* having identified the hsp for the current query sequence, print out the following:
- query sequence name
- hit sequence name
- length of the query
sequence covered by the hsp
- an alignment of the query and hit sequences making up that hsp