From 5a5d89d3881cb0d9014168845d96e5eebeb2bd42 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 31 Mar 2014 13:27:06 -0400 Subject: Add feature to have a top-scores file. closes issue #21 --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index 665e8b7..9ec3d47 100644 --- a/README.md +++ b/README.md @@ -120,6 +120,7 @@ background | Not Enabled | path of background file max\_consecutive\_binding | 4 | The maxium number of consecutive binding nucleotides in homodimer and heterodimers fg\_weight | 0 | How much extra weight to give higher frequency mers in fg. see "equations" (between 0 and 1) primer\_weight | 0 | How much extra weight to give to sets with a higher number of priemrs. (between 0 and 1) +output\_top\_nb | 10000 | How many scores do you want to output in your sorted output file? ## Equations @@ -169,7 +170,9 @@ The file structure outputted by default is this:    ├── $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 +    ├── selected-mers # final filtered mers used for select_mers.py +    ├── all-scores #file outputted by score_mers.py (all the scores generated) +    └── top-scores # the sorted top $output_top_nb scores from all-scores ### select\_mers.py output -- cgit v1.2.3