From 3fac0018e4da937dfa32b869f6ca819a6b67fe13 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Tue, 1 Apr 2014 13:32:17 -0400 Subject: add section for rescoring --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'README.md') diff --git a/README.md b/README.md index 5bdffda..45fd3d9 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,7 @@ PI: http://brisson.bio.upenn.edu/ * [Running Individual Steps](#running-individual-steps) * [Manually Scoring Specific Mer Combinations From List ](#manually-scoring-specific-mer-combinations-from-list) * [Manually Score All Combinations From List](#manually-score-all-combinations-from-list) + * [Manually Rescore All Combinations From Previously Scored File](#manually-rescore-all-combinations-from-previously-scored-file) * [Table of Tunable Parameters](#tunable-parameters) * [Equations](#equations) * [Mer Selectivity](#mer-selectivity) @@ -129,6 +130,16 @@ The mer file should look like this: each row is a separate mer. do not put multiple mers on one line. +### Manually rescore all combinations from previously scored file + +Users can manually rescore all combinations of mers they previously used in the +score\_mers.py script. This allows users to test different score functions easily +with the same combinations. + +An example would be this: + + score_func=nb_primers**2 score_mers.py -f fg.fa -b bg.fa -r fg_bg/run_1/all-scores -o primers_squared_scores + ## Tunable Parameters -- cgit v1.2.3