From b9fd58701ae7f50c5dda065f98cfd093263ec5a5 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 17 Apr 2014 11:16:49 -0400 Subject: update filter call --- SelectiveWholeGenomeAmplification | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'SelectiveWholeGenomeAmplification') diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification index c92f850..0521ef5 100755 --- a/SelectiveWholeGenomeAmplification +++ b/SelectiveWholeGenomeAmplification @@ -253,7 +253,7 @@ if [[ ! -d "$output_directory/$current_run/passes-filter" ]]; then fi echo "Outputting current run parameters" - 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 + 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 dna_con na_con mg_con dntps_con foreground background; do echo "$var" "${!var}" >> "$output_directory"/"$current_run"/parameters done; @@ -314,7 +314,7 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then check_non_empty "$average_binding" "average binding" echo " filtering mers that are not in the melting range ($min_melting_temp-$max_melting_temp)" - filter_melting_temperature.py "$min_melting_temp" "$max_melting_temp" < "$average_binding" > "$non_melting" || exit 1 + filter_melting_temperature.py -m "$min_melting_temp" -x "$max_melting_temp" -d "$dna_con" -g "$mg_con" -n "$na_con" -p "$dntps_con" < "$average_binding" > "$non_melting" || exit 1 check_non_empty "$non_melting" "melting temperature" echo " filtering mers that have more consecutive binding mers than allowed ($max_consecutive_binding)" -- cgit v1.2.1