add working remove mers from file

2 files changed, 9 insertions, 6 deletions

diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index 37ddeb1..23b14bc 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -27,7 +27,7 @@ check_mers() {
 	local counts="$2"
 	local mer=0
 
-	echo "  counting mers in $fasta_file:e"
+	echo "  counting mers in $fasta_file:"
 	echo -e "\e[32m"
 
 	#  remove the counts file so we can concatenate
@@ -315,11 +315,11 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then
 				# check mers from next ignore file
 				counts="$counts_directory/ignore-"$(basename "$ignore_file")
 				check_mers "$ignore_file" "$counts"
+				counts="$counts-counts"
 
 				echo "  filtering ignored mers from: $ignore_file"
-				cat "$ignore_all_mers_counts" | remove_mers_from_file.py "$ignore_file"> "$ignore_all_mers_counts-tmp"
+				cat "$ignore_all_mers_counts" | remove_mers_from_file.py "$counts"> "$ignore_all_mers_counts-tmp"
 				mv "$ignore_all_mers_counts-tmp" "$ignore_all_mers_counts"
-				read
 				check_non_empty "$ignore_all_mers_counts" "ignore all mers from file $ignore_file"
 			else 
 				echo "  $ignore_file not found, continuing..."
diff --git a/src/remove_mers_from_file.py b/src/remove_mers_from_file.py
index bef3ea3..3576e35 100755
--- a/src/remove_mers_from_file.py
+++ b/src/remove_mers_from_file.py
@@ -8,9 +8,12 @@ if __name__ == "__main__":
 	
 	mers_to_delete = set()
 
-	for mer in open(sys.argv[1], 'r'):
-		mer = mer.strip().split()[0]
-		mers_to_delete.add(mer)
+	for mer in open(sys.argv[1], 'rU'):
+		sp = mer.strip().split()
+		if len(sp) == 2:
+			mer = sp[0]
+			mers_to_delete.add(mer)
+
 
 	for line in sys.stdin:
 		if line.split()[0] not in mers_to_delete: