From 3cc69d19ef263b16cc1dc555c28fced86ea890f0 Mon Sep 17 00:00:00 2001 From: Surya Saha Date: Mon, 11 May 2015 14:18:51 -0400 Subject: [PATCH] made it customizable via params --- scripts/run_nucmer.sh | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/scripts/run_nucmer.sh b/scripts/run_nucmer.sh index 6315224..24f9322 100755 --- a/scripts/run_nucmer.sh +++ b/scripts/run_nucmer.sh @@ -6,21 +6,25 @@ usage(){ echo "usage: - $0 " + $0 + Recommend 100 bp word size and 500 bp min cluster size. Default word size is 20 amd default min cluster size is 65" exit 1 } -if [ "$#" -ne 2 ] +if [ "$#" -ne 4 ] then usage fi printf "Query : %s \n" "$1" printf "Reference : %s \n" "$2" -printf "Searching with word size of 100 and min cluster size of 500bp\n\n" -nucmer -l 100 -c 500 --noextend -p 500bp_qry_"${1}"__ref_"${2}" "$2" "$1" +printf "Word size : %s \n" "$3" +printf "Min cluster size : %s \n" "$4" +printf "Searching with word size of %i and min cluster size of %i\n\n" "$3" "$4" + +nucmer -l "$3" -c "$4" --noextend -p "${3}"bp_qry_"${1}"__ref_"${2}" "$2" "$1" #delta-filter -l 500 -u 99 500bp_qry_"${1}"__ref_"${2}".delta > 500bp_qry_"${1}"__ref_"${2}".delta.filtered -delta-filter -l 500 500bp_qry_"${1}"__ref_"${2}".delta > 500bp_qry_"${1}"__ref_"${2}".delta.filtered -show-coords -c -d -l -q -T -o 500bp_qry_"${1}"__ref_"${2}".delta.filtered > 500bp_qry_"${1}"__ref_"${2}".delta.filtered.coords +delta-filter -l "$3" "${3}"bp_qry_"${1}"__ref_"${2}".delta > "${3}"bp_qry_"${1}"__ref_"${2}".delta.filtered +show-coords -c -d -l -q -T -o "${3}"bp_qry_"${1}"__ref_"${2}".delta.filtered > "${3}"bp_qry_"${1}"__ref_"${2}".delta.filtered.coords -printf "\n\nOutput in %s \n" 500bp_qry_"${1}"__ref_"${2}".delta.filtered.coords +printf "\n\nOutput in %s \n" "${3}"bp_qry_"${1}"__ref_"${2}".delta.filtered.coords