From 06fa848b90982ddcd4308bb88d70a0d5f11f785b Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Tue, 25 Mar 2014 16:33:36 -0400 Subject: add average binding filter --- SelectiveGenomeAmplification | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) (limited to 'SelectiveGenomeAmplification') diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index b3bde4d..b66d06c 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -41,8 +41,8 @@ fi : ${max_melting_temp=30} : ${min_melting_temp=0} -# minimum mer count -: ${min_mer_count=0} +# minimum average binding distance in the foreground +: ${min_foreground_binding_average=50000} # maximum mers to pick : ${max_select=15} @@ -62,7 +62,7 @@ export max_mer_range export max_select -export min_mer_count +export min_foreground_binding_average export max_mer_distance export max_melting_temp @@ -130,17 +130,21 @@ for var in ignore_mers min_mer_range max_check cpus max_consecutive_binding max_ echo $var "${!var}" >> $output_directory/$current_run/parameters done; -non_melting=$output_directory/$current_run/`basename $foreground`-counts-non-melting-$min_melting_temp-$max_melting_temp -filtered_binding=$output_directory/$current_run/`basename $foreground`-counts-filtered-binding-$min_melting_temp-$max_melting_temp +average_binding=$output_directory/$current_run/`basename $foreground`-counts-average-binding +consecutive_binding=$output_directory/$current_run/`basename $foreground`-counts-consecutive-binding +non_melting=$output_directory/$current_run/`basename $foreground`-counts-non-melting + +echo "checking if mers appear at least as often in the fg as the average binding site or more $min_foreground_binding_average" +cat $fg_counts | filter_average_binding.py $foreground $min_foreground_binding_average > $average_binding || exit 1 echo "checking if mers are within the melting range $min_melting_temp $max_melting_temp" -cat $fg_counts | below_melting_temperature.py $min_melting_temp $max_melting_temp > $non_melting || exit 1 +cat $average_binding | filter_melting_temperature.py $min_melting_temp $max_melting_temp > $non_melting || exit 1 echo "filtering out elements that have more consecutive binding mers than allowed by \$max_consecutive_binding $max_consecutive_binding" -cat $non_melting | filter_max_consecutive_binding.py $max_consecutive_binding > $filtered_binding || exit 1 +cat $non_melting | filter_max_consecutive_binding.py $max_consecutive_binding > $consecutive_binding || exit 1 echo "scoring mer selectivity" -select_mers.py $non_melting $bg_counts > $selected || exit 1 +select_mers.py $consecutive_binding $bg_counts > $selected || exit 1 echo "scoring top mers based on selectivity" score_wrapper.sh $selected $foreground $background $output_directory/$current_run/scores-output || exit 1 -- cgit v1.2.3