From d00fc2bb1864c78fa926a5a84a693d4f84445723 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Tue, 4 Feb 2014 13:20:15 -0500 Subject: update save locations --- SelectiveGenomeAmplification | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'SelectiveGenomeAmplification') diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index fcbd5dd..d03ff96 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -122,20 +122,20 @@ if [ "$ignore_mers" ]; then fi echo "outputing current run parameters" -for var in ignore_mers min_mer_range max_mer_range max_select min_mer_count max_mer_distance max_melting_temp min_melting_temp foreground background; do +for var in ignore_mers min_mer_range max_consecutive_binding max_mer_range max_select min_mer_count max_mer_distance max_melting_temp min_melting_temp foreground background; do echo $var "${!var}" >> $output_directory/$current_run/parameters done; echo "checking if mers are within the melting range $min_melting_temp $max_melting_temp" -cat $fg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $fg_counts-non-melting -cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $bg_counts-non-melting +cat $fg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$foreground-counts-non-melting +cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$background-counts-non-melting echo "filtering out elements that have more consecutive binding mers than allowed by default $max_consecutive_binding" -cat $fg_counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $fg_counts-filtered-binding -cat $bg_counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $bg_counts-filtered-binding +cat $output_directory/$foreground-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$foreground-counts-filtered-binding +cat $output_directory/$background-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$background-counts-filtered-binding echo "scoring mer selectivity" -select_mers.py $fg_counts-filtered-binding $fg_tmp $bg_counts-filtered-binding $bg_tmp > $selected +select_mers.py $output_directory/$foreground-counts-filtered-binding $fg_tmp $output_directory/$background-counts-filtered-binding $bg_tmp > $selected echo "scoring top mers based on selectivity" score_mers.py $selected $fg_tmp $bg_tmp $output_directory/$current_run/scores-output -- cgit v1.2.3