From 4ef0f9a99c065d1d5c567001ffb9d81273147c40 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 27 Mar 2014 23:38:22 -0400 Subject: add docs for commit all combinations --- README.md | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c3aa6af..05dc5dc 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ valid steps are these: This function does not try to be smart, so use it wisely -### Manually scoring mer combinations +### Manually scoring specific mer combinations from file Users can manually score combinations of mers they choose using the score\_mers.py script. @@ -76,6 +76,26 @@ The combination file should look like this: each row is combination to be scored. + +### Manually score all combinations from file +Users can manually score all combinations of mers they choose using the +score\_mers.py script. + + score_mers.py -f foreground.fa -b background.fa -m mer file -o output + + +The mer file should look like this: + + ATATAT + TACATA + TACATAGCA + TATAGAATAC + CGTAGATA + TAGAAT + +each row is a seperate mer. do not put multiple mers on one line. + + ## Customizable variables range of mers, min and max -- cgit v1.2.3