diff options
Diffstat (limited to 'SelectiveGenomeAmplification')
| -rwxr-xr-x | SelectiveGenomeAmplification | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index 637ff2c..6010c08 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -147,6 +147,8 @@ done # output_top_nb, How many scored sets would you like in the top_scored_sets output file (Default = 10000)? : ${output_top_nb=10000} +# scoring_func: A custom scoring function. disable by default. See README.md + export ignore_mers export min_mer_range export max_mer_range @@ -231,7 +233,7 @@ if [[ ! -d "$output_directory/$current_run/filter" ]]; then fi echo "Outputting current run parameters" - for var in ignore_mers ignore_all_mers_from_files min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do + for var in scoring_func ignore_mers ignore_all_mers_from_files min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do echo "$var" "${!var}" >> "$output_directory"/"$current_run"/parameters done; @@ -323,8 +325,8 @@ if [[ -n "$step_score" ]] || [[ -n "$all" ]]; then # output our sorted scores echo "sorting and outputting top $output_top_nb scores" echo "top scores output file: $output_directory/$current_run/top-scores" - head -n 2 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores - tail -n +3 $output_directory/$current_run/all-scores | sort -r -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores + head -n 3 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores + tail -n +4 $output_directory/$current_run/all-scores | sort -r -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores fi |