From 4d69646fa3cec0fddb31a5b5e117b7a1ee003ab0 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 3 Apr 2014 00:13:06 -0400 Subject: add scoring to paramters --- SelectiveGenomeAmplification | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'SelectiveGenomeAmplification') diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index b19ef5b..e778cbd 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -147,7 +147,8 @@ done # output_top_nb, How many scored sets would you like in the top_scored_sets output file (Default = 10000)? : ${output_top_nb=10000} -# scoring_func: A custom scoring function. disable by default. See README.md +# score_func: A custom scoring function. disable by default. See README.md +: ${score_func="(nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio"} # sort score by the minimum or maximum value. acceptable parameters are min or max. : ${sort_by="min"} @@ -245,7 +246,7 @@ if [[ ! -d "$output_directory/$current_run/passes-filter" ]]; then fi echo "Outputting current run parameters" - for var in scoring_func ignore_mers ignore_all_mers_from_files min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do + for var in score_func ignore_mers ignore_all_mers_from_files min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do echo "$var" "${!var}" >> "$output_directory"/"$current_run"/parameters done; -- cgit v1.2.3