#!/bin/bash
#Author: Qunfeng Dong
#process PaCE result -> Running CAP3 from each PaCE cluster and process CAP3 result

echo "run cap3 on PaCE result"
./Cap3RescueMuFromPaCE.pl TIGRrepeatTrim_RescueMuGSS  RescueMuPlasmidAssembly.fsa estClust.66905.49.PaCE  > output
echo "extract cap3 result"
./RescueMuClusterExtract.pl CapAlign
sed "s/>CapAligntuc/>ZM_RM_GSStuc/g" CapAlign.alignment > ZM_RM_GSStuc.alignment 
rm -r -f  ZM_RM_GSStucAlignment
mkdir ZM_RM_GSStucAlignment
cp ZM_RM_GSStuc.alignment  ZM_RM_GSStucAlignment
cd ZM_RM_GSStucAlignment
../plantTUCMemAlign.pl  ZM_RM_GSStuc.alignment
mv *.TUC.fasta ../ZM_RM_GSS.TUC.fasta
cd ..
./RescueMuGSScontig_memberNum.pl ZM_RM_GSStuc.alignment > ZM_RM_GSS.TUC_GSS
./RescueMuTUG.pl ZM_RM_GSS.TUC.fasta CapAlign.TUS.fasta > ZM_RM_GSS.TUG.fasta
echo "All Completed! check out (1). ZM_RM_GSS.TUG.fast, (2).ZM_RM_GSS.TUC_GSS and (3). ZM_RM_GSStucAlignment "

echo "cap3 on gizmo3 is done " | mail -s "cap3 on RM parentals finished" qfdong@iastate.edu