diff pal_finder_wrapper_utils.sh @ 15:a3af1ff4cad1 draft

pal_finder 0.02.04.7 for testing.

--- a/pal_finder_wrapper_utils.sh	Thu Mar 22 07:21:26 2018 -0400
+++ b/pal_finder_wrapper_utils.sh	Mon May 14 11:10:19 2018 -0400
@@ -38,17 +38,21 @@
     # sequence ids where the PRIMER_PRODUCT_SIZE_RANGE has
     # upper limit which is smaller than lower limit
     local pr3in=$1
+    local outfile=$2
     local pattern="^(SEQUENCE_ID|PRIMER_PRODUCT_SIZE_RANGE)"
     for line in $(grep -E "$pattern" $pr3in | sed 's/ /^/' | sed 'N;s/\n/*/')
     do
 	# Loop over pairs of SEQUENCE_ID and PRIMER_PRODUCT_SIZE_RANGE
 	# keywords in the primer3 input
 	if [ ! -z "$(echo $line | grep ^SEQUENCE_ID)" ] ; then
-	    # Extract the values
+	    # Lines look like:
+	    # SEQUENCE_ID=(AT_1_16)(AT_1_16)M00879:99:000000000-AH9KG:1:2107:10006:2535*PRIMER_PRODUCT_SIZE_RANGE=194-329^59-194
 	    local size_range=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2 | tr '^' ' ')
 	    local seq_id=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2)
-	else
-	    local size_range=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2)
+	elif [ ! -z "$(echo $line | grep ^PRIMER_PRODUCT_SIZE_RANGE)" ] ; then
+	    # Lines look like:
+	    # PRIMER_PRODUCT_SIZE_RANGE=194-329^59-194*SEQUENCE_ID=(AT_1_16)(AT_1_16)M00879:99:000000000-AH9KG:1:2107:10006:2535
+	    local size_range=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2 | tr '^' ' ')
 	    local seq_id=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2)
 	fi
 	seq_id=$(echo $seq_id | cut -d')' -f3)
@@ -58,14 +62,14 @@
 	for range in $(echo $size_range) ; do
 	    local lower=$(echo $range | cut -d'-' -f1)
 	    local upper=$(echo $range | cut -d'-' -f2)
-	    if [ $lower -gt $upper ] ; then
+	    if [ "$lower" -gt "$upper" ] ; then
 		bad_range=yes
 		break
 	    fi
 	done
 	# Report if the range is wrong
 	if [ ! -z "$bad_range" ] ; then
-	    echo "$seq_id ($size_range)"
+	    echo "${seq_id}"$'\t'"(${size_range})" >>$outfile
 	fi
     done
 }