use kmer_continuous_count instead of kmer_total_count, remove tmp file, update parameters for select_mers.py

1 files changed, 8 insertions, 17 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
index bb52626..b3fdd2f 100755
--- a/SelectiveGenomeAmplification
+++ b/SelectiveGenomeAmplification
@@ -91,22 +91,15 @@ mkdir -p $output_directory/$current_run
 for fasta_file in $foreground $background; do
 
 	counts=$counts_directory/$(basename $fasta_file)
-	tmp=$tmp_directory/$(basename $fasta_file)
 
 	echo pre-processing $fasta_file
 
-	# check if our preprocessed file exists
-	if [[ ! -f $tmp ]]; then
-		echo "> pre processed $fasta_file" >> $tmp
-		cat $fasta_file | grep -v "^>" | tr -d '\n' >> $tmp
-	fi
-
 	# run counts if they haven't been created 
 	rm $counts-counts
 	for mer in `seq $min_mer_range $max_mer_range`;	do 
 		if [ ! -e $counts-counts-$mer ]; then
 			echo checking $mer mers for $fasta_file
-			kmer_total_count -i $tmp -k $mer -l -n >> $counts-counts-$mer
+			kmer_continuous_count -i $fasta_file -k $mer -l -n >> $counts-counts-$mer
 		else 
 			echo "$mer mers already done for $fasta_file"
 		fi
@@ -119,9 +112,6 @@ done
 fg_counts=$counts_directory/$(basename $foreground)-counts
 bg_counts=$counts_directory/$(basename $background)-counts
 
-fg_tmp=$tmp_directory/$(basename $foreground)
-bg_tmp=$tmp_directory/$(basename $background)
-
 selected=$output_directory/$current_run/selected-mers
 
 # remove ignored mers
@@ -139,15 +129,16 @@ for var in ignore_mers min_mer_range max_check cpus max_consecutive_binding max_
 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 > $output_directory/$current_run/$foreground-counts-non-melting 
-cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$current_run/$background-counts-non-melting 
+cat $fg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$current_run/`basename $foreground`-counts-non-melting  || exit 1
+cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$current_run/`basename $background`-counts-non-melting  || exit 1
 
 echo "filtering out elements that have more consecutive binding mers than allowed by default $max_consecutive_binding"
-cat $output_directory/$current_run/$foreground-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/$foreground-counts-filtered-binding
-cat $output_directory/$current_run/$background-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/$background-counts-filtered-binding
+cat $output_directory/$current_run/`basename $foreground`-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/`basename $foreground`-counts-filtered-binding || exit 1
+cat $output_directory/$current_run/`basename $background`-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/`basename $background`-counts-filtered-binding || exit 1
 
 echo "scoring mer selectivity"
-select_mers.py $output_directory/$current_run/$foreground-counts-filtered-binding $fg_tmp $output_directory/$current_run/$background-counts-filtered-binding $bg_tmp > $selected
+select_mers.py $output_directory/$current_run/`basename $foreground`-counts-filtered-binding \
+							 $output_directory/$current_run/`basename $background`-counts-filtered-binding > $selected || exit 1
 	
 echo "scoring top mers based on selectivity"
-score_mers.py $selected $fg_tmp $bg_tmp $output_directory/$current_run/scores-output
+score_mers.py $selected <(  cat $foreground | grep -v "^>" | tr -d '\n' ) <(  cat $background | grep -v "^>" | tr -d '\n') $output_directory/$current_run/scores-output || exit 1