From 01bec2e491ebc5756095ba69386c8a00bdb761cf Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 31 Mar 2014 16:01:52 -0400 Subject: update README.md for custom scoring --- README.md | 29 +++++++++++++++++++++++++---- 1 file changed, 25 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 9039949..5cfce11 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,9 @@ PI: http://brisson.bio.upenn.edu/ * [Table of Tunable Parameters](#tunable-parameters) * [Equations](#equations) * [Mer Selectivity](#mer-selectivity) - * [Scoring Equation](#score-function) + * [Scoring Combinations](#score-combinations) + * [Default Scoring Function](#default-scoring-function) + * [Custom Scoring Function](#custom-scoring-function) * [Output](#output) * [Select Mers](#select_merspy-output) * [Score Mers](#score_merspy-output) @@ -171,11 +173,11 @@ environmental variable if you wish to do so. (foreground hit / background hit) * (foreground hit ^ fg_weight) -### Score function +### Scoring combinations -The scoring function is this: +All variables used in our scoring function are described here: - fg_pts = all the points of each mer in the combination, and sequence ends + fg_pts = an array of all the points of each mer in the combination, and sequence ends fg_mean_dist = mean distance between each point in fg_pts fg_stddev = standard deviation of distance between each point in fg_pts @@ -184,8 +186,27 @@ The scoring function is this: bg_ratio = length of background / number of times primer was in background +#### Default score function + +The default scoring function is this: + mer_score = (nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio +#### Custom scoring function + +We support custom scoring via python's exec methods. This means that you can +destroy your system, blow up the universe, implode your hard drive, all within +the confinesof this exec. That means don't do anything crazy. Stick to basic arithmetic. + +This is a security hole. + +you can specify it like any other parameter like so: + + # the default function + scoring\_func="(nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio" SelectiveGenomeAmplification.... + +You need to use **valid** python code. + ## Output The file structure outputted by default is this: -- cgit v1.2.3