From e7b5672871b301dbcd3ced662a858f48fbc4c267 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 27 Mar 2014 23:56:52 -0400 Subject: more documentation --- README.md | 33 +++++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 05dc5dc..1cfbda3 100644 --- a/README.md +++ b/README.md @@ -57,8 +57,7 @@ valid steps are these: - select (3) - score (4) -This function does not try to be smart, so use it wisely - +This function does not try to be smart, so use it wisely. ### Manually scoring specific mer combinations from file @@ -141,3 +140,33 @@ environmental variable if you wish to do so. ### Score function + +The scoring function is this: + + fg_pts = all the points of each mer in the combination, and sequence ends4 + fg_mean_dist = mean distance between each point in fg_pts + fg_stddev = standard deviation of distance between each point in fg_pts + + nb_primers = number of primers in a combination + primer_weight = extra weight for sets with higher primers + + bg_ratio = length of background / number of times primer was in background + + mer_score = (nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio + +## Output + +The file structure outputted by default is this: + $foreground_$background/ + └── run_1 # current_run +    ├── filter # filter folder for filtering steps +    │   ├── 1-$foreground-ignore-mers +    │   ├── 2-$foreground-ignore-all-mers +    │   ├── 3-$foreground-average-binding +    │   ├── 4-$foreground-non-melting +    │   └── 5-$foreground-consecutive-binding +    ├── $foreground-filtered-counts # final filtered mers used for selected_mers.py +    ├── parameters # parameters used in the run +    ├── selected-mers # final filtered mers used for selected_mers.py +    └── scores-output # file outputted by score_mers.py + -- cgit v1.2.1