--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbsx_digest.sh	Tue Jan 26 07:38:36 2016 -0500
@@ -0,0 +1,153 @@
+#!/usr/bin/env bash
+
+#export PATH=$PATH:$(dirname $0)
+#BASEDIR=$(dirname $0)
+
+
+genome=$1
+length=$2 
+enzyme_combination=$3
+dualEnzyme="0"
+min_size=$4
+max_size=$5
+digest_bed=$6
+digest_result=$7
+
+awk 'BEGIN {n_seq=0;} /^>/ {if(n_seq%1==0){file=$1".fa"; sub(">","",file)} print >> file; n_seq++; print file >> "list.txt"; next;} { print >> file; }' < $genome 
+
+case "$enzyme_combination" in
+    ApeKI) 
+            enzyme="ApeKI"
+            cutsite="G^CWGC"
+    ;;
+    PstI) 
+            enzyme="PstI"
+            cutsite="CTGCA^G"
+    ;;
+    EcoT22I) 
+            enzyme="EcoT22I"
+            cutsite="ATGCA^T"
+    ;;
+    PasI) 
+            enzyme="PasI"
+            cutsite="CC^CWGGG"
+    ;;
+    HpaII) 
+            enzyme="HpaII"
+            cutsite="C^CGG"
+    ;;
+    MspI) 
+            enzyme="MspI"
+            cutsite="C^CGG"
+    ;;
+    PstI-EcoT22I) 
+            dualEnzyme="1"
+            enzyme="PstI"
+            cutsite="CTGCA^G"
+            enzyme2="EcoT22I"
+            cutsite2="ATGCA^T";
+    ;;
+    PstI-MspI) 
+            dualEnzyme="1"
+            enzyme="PstI"
+            cutsite="CTGCA^G"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    PstI-TaqI) 
+            dualEnzyme="1"
+            enzyme="PstI"
+            cutsite="CTGCA^G"
+            enzyme2="TaqI"
+            cutsite2="T^CGA"
+    ;;
+    SbfI-MspI) 
+            dualEnzyme="1"
+            enzyme="SbfI"
+            cutsite="CCTGCA^GG"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    AsiSI-MspI) 
+            dualEnzyme="1"
+            enzyme="AsiSI"
+            cutsite="GCCGAT^CGC"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    BssHII-MspI) 
+            dualEnzyme="1"
+            enzyme="BssHII"
+            cutsite="G^CGCGC"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    FseI-MspI) 
+            dualEnzyme="1"
+            enzyme="FseI"
+            cutsite="GGCCGG^CC"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    SalI-MspI) 
+            dualEnzyme="1"
+            enzyme="SalI"
+            cutsite="G^TCGAC"
+            enzyme2="MspI"
+            cutsite2="C^CGG"
+    ;;
+    ApoI) 
+            enzyme="ApoI"
+            cutsite="R^AATTY"
+    ;;
+    BamHI) 
+            enzyme="BamHI"
+            cutsite="G^GATCC"
+    ;;
+    MseI) 
+            enzyme="MseI"
+            cutsite="T^TAA"
+    ;;
+    Sau3AI) 
+            enzyme="Sau3AI"
+            cutsite="^GATC"
+    ;;
+    RBSTA) 
+            enzyme="RBSTA"
+            cutsite="^TA"
+    ;;
+    RBSCG) 
+            enzyme="RBSCG"
+            cutsite="^CG"
+    ;;
+    NspI) 
+            enzyme="NspI"
+            cutsite="RCATG^Y"
+    ;;
+    AvaII) 
+            enzyme="AvaII"
+            cutsite="G^GWCC"
+    ;;
+esac
+
+extraparameters="";
+if [ "$dualEnzyme" != "0" ];
+then
+    extraparameters="-E $enzyme2 -D $cutsite2";
+fi
+
+perl $GBSX_PATH/GBSX_digest.pl -f list.txt -l $length -d $cutsite -e $enzyme $extraparameters -n $min_size -m $max_size;
+
+rm *.fa;
+rm list.txt;
+
+if [ "$dualEnzyme" != "0" ];
+then
+    cat "genome."$enzyme"."$enzyme2"."$length"nt.digest.bed" > $digest_bed;
+    cat "genome."$enzyme"."$enzyme2"."$length"nt.digest_results" > $digest_result;
+else
+    cat "genome."$enzyme"."$length"nt.digest.bed" > $digest_bed;
+    cat "genome."$enzyme"."$length"nt.digest_results" > $digest_result;
+fi
+
+