Notes on 'matrix' files
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09 Feb. 2005, Gordon Robertson, grobertson@bcgsc.ca


> 'matrix' file format for pairwise distances
1 1 0.000
2 1 0.519
2 2 0.000
3 1 0.627
3 2 0.592
3 3 0.000
...

> Columns: id1 id2  pairwise_distance
> separated by one space

- for Melanie (UBC), we need to add in an initial line that is how many 'things' gave the pairwise distances.


> id's are from Keven's DB on the GSC's db01
db: cisred_motifs_50PWM_100genes_th70
db: cisred_motifs_all_200genes_th85
- in each DB, in the 'features' table
	- 'id' column has 'id's
	- 'feature' column has JASPAR PWM names

> Distances are from Misha's 'edit distance' formula for 'hit-stacks'