From cb87a369533d7619ef8c7ce292cc20546f1ae208 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 28 Mar 2014 00:06:11 -0400 Subject: add docs --- README.md | 49 ++++++++++++++++++++++++++++++++----------------- 1 file changed, 32 insertions(+), 17 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 1cfbda3..32f93db 100644 --- a/README.md +++ b/README.md @@ -144,29 +144,44 @@ environmental variable if you wish to do so. 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 + 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 + 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 + 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 + $foreground_$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 select_mers.py +    ├── parameters # parameters used in the run +    ├── selected-mers # final filtered mers used for select_mers.py +    └── scores-output # file outputted by score_mers.py +### select\_mers.py output + +Select mers outputs a tab delimited file, with 4 columns: mer foreground count +background count and the mer selectivity we give it. (higher is better) + + CTAACTTAGGTC 1572 155 10.14194 + CTAACATAGGTC 1479 132 11.20455 + GACCTATGTTAG 1479 132 11.20455 + + +### score\_mers.py output + +score medrs outputs a tab delmited file with 6 columns: + + nb_primers Combination Score FG_mean_dist FG_stdev_dist BG_ratio -- cgit v1.2.1